Contacts of the helix formed by residues 31 - 54 (chain H) in PDB entry 1GN2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 31 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G ASN* 3.6 45.3 - - + +
27H LEU* 2.8 32.8 + - + +
29H HIS 3.3 0.2 - - - -
30H SER* 1.3 92.0 + - - +
32H HIS* 1.3 63.7 + - - +
33H HIS 3.6 0.2 - - - -
34H ALA* 3.9 1.6 - - - +
35H THR* 2.8 31.9 + - - -
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Residues in contact with HIS 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163G GLU* 4.2 6.3 + - - -
167G TYR* 2.6 38.9 + + - -
172G ASN* 3.7 23.9 - - + +
27H LEU 3.1 18.4 + - - -
28H HIS* 3.3 25.6 - + + +
31H LYS* 1.3 76.9 - - - +
33H HIS* 1.3 68.1 + - - +
35H THR* 3.1 16.3 + - - -
36H TYR* 3.2 25.1 + - + -
164H HIS* 3.7 34.5 + + + +
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Residues in contact with HIS 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 3.8 9.2 - - + +
7H PRO* 3.8 12.4 - - + +
28H HIS 2.9 15.8 + - - +
29H HIS* 3.3 15.4 + - - +
32H HIS* 1.3 73.1 - - - +
34H ALA* 1.3 63.9 + - - +
36H TYR* 3.1 19.7 + - + +
37H VAL* 3.1 20.3 + - + +
73H HIS* 3.1 33.8 + - - -
76H HIS* 3.0 32.5 - + + +
77H THR* 3.4 17.9 + - - -
80H TRP* 2.9 27.1 + + - +
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Residues in contact with ALA 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LEU* 3.8 26.0 - - + +
29H HIS 3.3 3.6 + - - -
30H SER 3.5 24.7 - - - +
31H LYS 3.6 2.4 + - - +
32H HIS 3.2 0.4 - - - -
33H HIS* 1.3 78.6 - - - +
35H THR* 1.3 58.1 + - - +
37H VAL* 3.4 7.2 + - - +
38H LYS* 3.0 28.1 + - - +
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Residues in contact with THR 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LYS 2.8 16.4 + - - -
32H HIS* 3.1 12.1 + - - +
33H HIS 3.1 0.4 - - - -
34H ALA* 1.3 78.2 - - - +
36H TYR* 1.3 65.1 + - + +
38H LYS* 3.5 6.9 + - - +
39H GLY* 3.0 23.0 + - - -
69H ASN* 4.3 3.9 - - - +
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Residues in contact with TYR 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H HIS* 3.2 30.2 + - + -
33H HIS* 3.1 13.5 + - - +
35H THR* 1.3 79.6 - - + +
37H VAL* 1.3 56.7 + - - +
39H GLY* 3.1 1.0 + - - -
40H ALA* 2.7 36.6 + - - +
68H PHE* 4.0 18.1 - + - -
69H ASN* 3.5 25.5 - - - +
72H GLY* 4.0 10.5 - - - -
73H HIS* 3.8 18.6 - - - +
76H HIS* 3.6 24.7 - + - -
145H HIS* 2.7 38.1 + + - -
162H TRP* 3.8 19.2 - - - -
164H HIS* 4.4 6.1 - + - -
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Residues in contact with VAL 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H TYR* 3.7 24.4 - - - +
5H THR* 4.1 0.4 - - - -
6H LEU* 3.9 26.5 - - + +
33H HIS* 3.1 17.6 + - + +
34H ALA* 3.6 9.0 - - - +
36H TYR* 1.3 81.8 - - - +
38H LYS* 1.3 63.8 + - - +
40H ALA* 3.8 5.7 - - - +
41H ASN* 3.1 27.4 + - - +
73H HIS* 3.5 37.5 - - + +
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Residues in contact with LYS 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ALA 3.0 17.3 + - - +
35H THR* 3.9 6.3 - - + +
36H TYR 3.2 0.2 - - - -
37H VAL* 1.3 79.6 - - - +
39H GLY* 1.3 60.1 + - - +
41H ASN* 3.2 7.3 + - + +
42H ASP* 2.9 61.2 + - - +
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Residues in contact with GLY 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H THR 3.0 14.8 + - - -
36H TYR 3.1 3.8 + - - -
38H LYS* 1.3 81.5 - - - +
40H ALA* 1.3 55.7 + - - +
42H ASP* 3.5 7.2 + - - +
43H ALA* 3.0 30.0 + - - +
65H ASN* 5.6 0.2 - - - +
69H ASN* 3.6 22.7 + - - -
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Residues in contact with ALA 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H TYR* 3.8 24.5 - - + -
36H TYR 2.7 20.3 + - - +
37H VAL* 3.8 7.4 - - - +
38H LYS 3.2 0.2 - - - -
39H GLY* 1.3 70.0 - - - +
41H ASN* 1.3 66.3 + - - +
43H ALA* 3.3 5.1 + - - +
44H VAL* 3.1 27.4 + - - +
66H LEU* 4.7 2.3 - - + +
69H ASN* 3.4 18.8 - - - +
70H LEU* 4.1 14.6 - - + +
73H HIS* 5.0 2.0 - - + -
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Residues in contact with ASN 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F LYS* 5.0 0.9 + - - -
3H GLU* 3.7 27.2 + - + +
4H TYR* 2.8 58.1 + - - +
37H VAL* 3.1 18.6 + - - +
38H LYS* 3.7 8.1 - - + +
40H ALA* 1.3 76.8 - - - +
42H ASP* 1.3 64.4 + - - +
44H VAL* 3.1 10.4 + - - +
45H ALA* 3.0 21.5 + - - +
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Residues in contact with ASP 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H LYS* 2.9 58.3 + - - +
39H GLY* 3.8 7.4 - - - +
41H ASN* 1.3 76.3 - - - +
43H ALA* 1.3 58.6 + - - +
45H ALA* 3.1 8.1 + - - +
46H LYS* 2.9 34.8 + - + +
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Residues in contact with ALA 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLY 3.0 18.1 + - - +
40H ALA* 3.6 5.8 - - - +
41H ASN 3.2 0.2 - - - -
42H ASP* 1.3 75.3 - - - +
44H VAL* 1.3 64.1 + - - +
46H LYS* 3.3 7.6 + - - +
47H LEU* 3.3 28.7 + - - +
62H ASN* 4.5 4.4 + - - +
65H ASN* 4.0 12.8 - - + +
66H LEU* 3.6 38.4 - - + +
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Residues in contact with VAL 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F LYS* 4.6 16.4 - - + +
138F LEU* 4.8 12.3 - - + -
4H TYR* 4.0 20.2 - - + -
40H ALA 3.1 14.3 + - - +
41H ASN* 3.4 9.4 - - - +
43H ALA* 1.3 79.2 - - - +
45H ALA* 1.3 63.4 + - + +
47H LEU* 3.3 17.8 + - - +
48H GLU* 3.3 27.1 + - - +
51H ARG* 4.9 1.2 + - - -
66H LEU* 4.0 17.9 - - + -
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Residues in contact with ALA 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ASN 3.0 13.1 + - - +
42H ASP* 3.1 10.3 + - - +
44H VAL* 1.3 79.2 - - + +
46H LYS* 1.3 64.5 + - - +
48H GLU* 2.9 27.5 + - - +
49H GLU* 2.9 15.4 + - - +
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Residues in contact with LYS 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E SER* 6.5 1.3 - - - -
42H ASP* 2.9 19.5 + - + +
43H ALA* 3.3 6.9 + - - +
45H ALA* 1.3 76.0 - - + +
47H LEU* 1.3 52.4 + - - +
49H GLU* 3.5 33.1 + - - +
50H ALA* 2.8 34.8 + - - +
62H ASN* 3.6 28.7 - - - +
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Residues in contact with LEU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F GLN* 4.1 23.6 - - - +
138F LEU* 6.4 0.9 - - + -
43H ALA 3.3 19.0 + - - +
44H VAL* 3.6 10.1 - - - +
45H ALA 3.0 0.6 - - - -
46H LYS* 1.3 75.3 - - - +
48H GLU* 1.3 55.8 + - - +
50H ALA* 3.1 7.6 + - + +
51H ARG* 2.7 53.9 + - - +
56H HIS* 4.9 2.0 - - + +
59H ILE* 4.3 15.7 - - + -
62H ASN* 3.8 39.7 - - + +
63H GLU* 4.7 4.5 - - - +
66H LEU* 4.1 22.4 - - + -
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Residues in contact with GLU 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H VAL* 3.3 24.7 + - - +
45H ALA* 2.9 18.6 + - - +
47H LEU* 1.3 76.5 - - - +
49H GLU* 1.3 60.8 + - - +
51H ARG* 3.0 26.6 + - - +
52H ALA* 2.8 30.6 + - - +
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Residues in contact with GLU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H ALA 2.9 10.6 + - - +
46H LYS* 3.8 35.5 + - - +
48H GLU* 1.3 83.6 - - + +
50H ALA* 1.3 61.8 + - - +
52H ALA* 3.5 5.2 + - - +
53H LYS* 3.1 59.1 + - + +
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Residues in contact with ALA 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H LYS 2.8 19.1 + - - +
47H LEU* 3.5 9.4 - - + +
48H GLU 3.1 0.2 - - - -
49H GLU* 1.3 77.8 - - - +
51H ARG* 1.3 62.5 + - - +
53H LYS* 3.7 2.2 + - - +
54H GLU* 3.1 2.8 + - - -
55H ASP 3.1 45.3 + - - +
56H HIS* 3.9 19.0 - - + +
62H ASN* 4.3 11.9 - - - +
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Residues in contact with ARG 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ALA 3.9 12.6 + - - -
103F PHE* 3.7 43.6 + - - +
108F LYS* 4.1 37.6 - - + +
112F GLN* 2.7 43.3 + - - +
44H VAL 4.9 1.2 + - - -
47H LEU* 2.7 27.9 + - - +
48H GLU* 3.4 39.5 + - - +
50H ALA* 1.3 77.4 - - - +
52H ALA* 1.3 63.8 + - - +
54H GLU* 3.4 12.1 + - - +
56H HIS* 4.0 17.7 - - + +
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Residues in contact with ALA 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F LYS* 4.4 15.1 + - - +
48H GLU 2.8 15.0 + - - +
49H GLU* 3.8 7.2 - - - +
51H ARG* 1.3 79.1 - - - +
53H LYS* 1.3 65.4 + - + +
54H GLU* 3.1 8.9 + - - +
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Residues in contact with LYS 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H GLU* 3.1 43.6 + - + +
50H ALA* 5.2 0.9 - - - +
52H ALA* 1.3 76.7 - - + +
54H GLU* 1.3 76.6 + - - +
55H ASP* 4.1 22.9 - - + +
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Residues in contact with GLU 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F LYS* 5.5 7.2 - - + -
50H ALA 3.1 6.2 + - - -
51H ARG* 3.4 9.1 + - - +
52H ALA 3.1 11.9 - - - +
53H LYS* 1.3 84.3 - - - +
55H ASP* 1.3 57.1 + - - +
56H HIS* 4.1 6.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il