Contacts of the helix formed by residues 31 - 54 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ASN* 3.5 44.9 - - + +
27D LEU* 2.8 31.6 + - + +
29D HIS 3.4 0.2 - - - -
30D SER* 1.3 90.3 + - - +
32D HIS* 1.3 63.9 + - - +
34D ALA* 3.6 2.0 + - - +
35D THR* 2.8 30.9 + - - -
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Residues in contact with HIS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C GLU* 4.3 5.2 - - - -
167C TYR* 2.8 39.3 + + - -
172C ASN* 3.5 24.5 - - + +
27D LEU 3.1 18.6 + - - -
28D HIS* 3.3 25.6 - - + +
31D LYS* 1.3 77.3 - - - +
33D HIS* 1.3 66.8 + - - +
35D THR* 3.1 15.7 + - - -
36D TYR* 3.2 25.5 + - + -
76D HIS* 5.2 0.2 - - - +
164D HIS* 3.7 33.5 + + + +
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Residues in contact with HIS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 3.8 8.3 - - + +
7D PRO* 3.8 12.4 - - + +
28D HIS 2.9 15.4 + - - +
29D HIS* 3.3 15.0 - - - +
31D LYS 3.6 0.2 - - - -
32D HIS* 1.3 74.1 - - - +
34D ALA* 1.3 63.5 + - - +
36D TYR* 3.1 19.1 + - + +
37D VAL* 3.1 19.7 + - + +
73D HIS* 3.1 33.5 + - - -
76D HIS* 3.0 32.2 - + + +
77D THR* 3.4 17.9 - - - -
80D TRP* 2.9 27.1 + + - +
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 3.8 25.8 - - + -
29D HIS 3.3 4.0 + - - -
30D SER 3.5 24.7 - - - +
31D LYS 3.9 2.5 - - - +
32D HIS 3.2 0.4 - - - -
33D HIS* 1.3 78.8 - - - +
35D THR* 1.3 58.2 + - - +
37D VAL* 3.4 6.8 + - - +
38D LYS* 3.0 27.7 + - - +
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Residues in contact with THR 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LYS 2.8 17.1 + - - -
32D HIS* 3.1 12.5 + - - -
33D HIS 3.1 0.2 - - - -
34D ALA* 1.3 78.7 - - - +
36D TYR* 1.3 63.7 + - + +
38D LYS* 3.5 7.0 + - - +
39D GLY* 3.0 23.6 + - - -
69D ASN* 4.3 3.7 - - - +
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Residues in contact with TYR 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D HIS* 3.2 30.6 + - + -
33D HIS* 3.1 13.9 + + - +
35D THR* 1.3 78.5 - - + +
37D VAL* 1.3 57.8 + - - +
39D GLY* 3.1 0.7 + - - -
40D ALA* 2.7 36.9 + - - +
68D PHE* 4.0 18.5 - + - -
69D ASN* 3.5 25.8 - - - +
72D GLY* 4.0 10.3 - - - -
73D HIS* 3.8 18.8 - - - +
76D HIS* 3.6 24.5 - + - -
145D HIS* 2.7 38.5 + + - -
162D TRP* 3.8 18.7 - - - -
164D HIS* 4.4 5.9 - + - -
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Residues in contact with VAL 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D TYR* 3.7 24.4 - - - +
5D THR* 4.1 0.2 - - - -
6D LEU* 3.9 25.6 - - + +
33D HIS* 3.1 17.6 + - + +
34D ALA* 3.6 9.9 - - - +
36D TYR* 1.3 80.1 - - - +
38D LYS* 1.3 65.6 + - + +
40D ALA* 3.8 6.3 - - - +
41D ASN* 3.1 26.5 + - - +
73D HIS* 3.5 37.7 - - + +
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Residues in contact with LYS 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ALA 3.0 16.4 + - - +
35D THR* 3.9 6.7 - - - +
37D VAL* 1.3 79.8 - - + +
39D GLY* 1.3 60.9 + - - +
41D ASN* 3.2 7.5 + - + +
42D ASP* 2.9 60.5 + - - +
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Residues in contact with GLY 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D THR 3.0 15.7 + - - -
36D TYR 3.1 3.6 + - - -
38D LYS* 1.3 82.3 - - - +
40D ALA* 1.3 56.3 + - - +
42D ASP* 3.8 7.2 - - - +
43D ALA* 3.0 29.5 + - - +
65D ASN* 5.6 0.2 - - - +
69D ASN* 3.6 22.3 + - - -
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D TYR* 3.8 24.2 - - + -
36D TYR 2.7 19.2 + - - +
37D VAL* 3.8 7.6 - - - +
38D LYS 3.2 0.4 - - - -
39D GLY* 1.3 68.7 - - - +
41D ASN* 1.3 67.3 + - - +
43D ALA* 3.3 5.3 + - - +
44D VAL* 3.1 27.5 + - - +
66D LEU* 4.7 2.1 - - + +
69D ASN* 3.4 19.4 - - - +
70D LEU* 4.1 14.1 - - + +
73D HIS* 5.0 2.7 - - + -
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Residues in contact with ASN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS* 4.9 1.2 + - - -
3D GLU* 3.7 26.7 + - + +
4D TYR* 2.8 57.5 + - - +
37D VAL* 3.1 19.4 + - - +
38D LYS* 3.7 8.5 - - + +
40D ALA* 1.3 76.8 - - - +
42D ASP* 1.3 64.7 + - - +
44D VAL* 3.1 9.5 + - - +
45D ALA* 3.0 21.8 + - - +
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Residues in contact with ASP 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LYS* 2.9 62.0 + - - +
39D GLY* 3.8 6.9 - - - +
41D ASN* 1.3 72.7 - - - +
43D ALA* 1.3 58.5 + - - +
45D ALA* 3.1 8.6 + - - +
46D LYS* 2.9 34.3 + - + +
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D GLY 3.0 17.7 + - - +
40D ALA 3.6 5.4 - - - +
41D ASN 3.2 0.2 - - - -
42D ASP* 1.3 76.8 - - - +
44D VAL* 1.3 64.2 + - - +
46D LYS* 3.3 7.6 + - - +
47D LEU* 3.3 28.9 + - - +
62D ASN* 4.5 5.1 + - - +
65D ASN* 4.0 11.9 - - + -
66D LEU* 3.6 38.1 - - + +
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS* 4.2 20.2 - - + +
138B LEU* 4.7 13.9 - - + -
4D TYR* 4.0 20.0 - - + +
40D ALA 3.1 13.8 + - - +
41D ASN* 3.1 10.1 + - - +
43D ALA* 1.3 78.6 - - - +
45D ALA* 1.3 65.4 + - - +
47D LEU* 3.3 17.7 + - - +
48D GLU* 3.3 26.7 + - - +
51D ARG* 4.9 1.2 + - - -
66D LEU* 4.0 17.5 - - + -
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Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASN 3.0 13.1 + - - +
42D ASP* 3.1 10.9 + - - +
44D VAL* 1.3 79.2 - - + +
46D LYS* 1.3 63.7 + - + +
48D GLU* 2.9 27.3 + - - +
49D GLU* 2.9 14.7 + - - +
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Residues in contact with LYS 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER* 6.5 0.7 - - - -
42D ASP* 2.9 19.1 + - + +
43D ALA* 3.8 5.6 - - - +
45D ALA* 1.3 76.4 - - + +
47D LEU* 1.3 52.5 + - - +
49D GLU* 3.5 34.8 + - - +
50D ALA* 2.8 34.2 + - - +
62D ASN* 3.6 28.9 - - - +
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Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B GLN* 3.9 26.7 - - - +
138B LEU* 6.0 3.1 - - + -
43D ALA 3.3 18.0 + - - +
44D VAL* 3.6 11.0 - - - +
45D ALA 3.0 0.8 - - - -
46D LYS* 1.3 75.5 - - - +
48D GLU* 1.3 55.7 + - - +
50D ALA* 3.5 7.0 - - + +
51D ARG* 2.7 54.2 + - - +
56D HIS* 4.9 1.1 - - + -
59D ILE* 4.3 13.2 - - + -
62D ASN* 3.8 39.0 - - + +
63D GLU* 4.7 4.0 - - - +
66D LEU* 4.1 22.4 - - + -
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Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D VAL* 3.3 24.8 + - - +
45D ALA* 2.9 18.9 + - - +
47D LEU* 1.3 78.4 - - - +
49D GLU* 1.3 61.5 + - - +
51D ARG* 3.0 26.5 + - - +
52D ALA* 2.8 30.9 + - - +
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Residues in contact with GLU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ALA 2.9 10.7 + - - +
46D LYS* 3.8 36.3 + - - +
48D GLU* 1.3 82.4 - - - +
50D ALA* 1.3 62.5 + - - +
52D ALA* 3.8 5.1 - - - +
53D LYS* 3.1 59.2 + - + +
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Residues in contact with ALA 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LYS 2.8 18.7 + - - +
47D LEU* 3.5 9.2 - - + +
48D GLU 3.1 0.2 - - - -
49D GLU* 1.3 77.8 - - - +
51D ARG* 1.3 62.0 + - - +
53D LYS* 3.7 2.8 + - - +
54D GLU* 3.1 3.5 + - - -
55D ASP* 3.1 45.4 + - - +
56D HIS* 3.9 18.9 - - + +
62D ASN* 4.3 12.1 - - - +
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Residues in contact with ARG 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA 3.6 19.3 + - - -
103B PHE* 3.6 45.9 + - - +
108B LYS* 3.9 34.7 - - + +
112B GLN* 3.0 34.2 + - - +
44D VAL 4.9 1.0 + - - -
47D LEU* 2.7 28.0 + - - +
48D GLU* 3.0 39.7 + - - +
50D ALA* 1.3 77.0 - - - +
52D ALA* 1.3 64.3 + - - +
54D GLU* 3.4 11.1 + - - +
56D HIS* 4.0 15.5 - - + +
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Residues in contact with ALA 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LYS* 4.2 15.9 + - - +
48D GLU 2.8 15.9 + - - +
49D GLU* 3.8 6.7 - - - +
51D ARG* 1.3 79.1 - - - +
53D LYS* 1.3 65.3 + - + +
54D GLU* 3.1 8.4 + - - +
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Residues in contact with LYS 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLU* 3.1 43.2 + - + +
50D ALA* 5.2 0.9 - - - +
52D ALA* 1.3 77.1 - - + +
54D GLU* 1.3 76.2 + - - +
55D ASP* 3.3 22.0 + - + +
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Residues in contact with GLU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LYS* 5.1 10.8 - - + -
50D ALA 3.1 7.1 + - - -
51D ARG* 3.4 8.5 + - - +
52D ALA 3.1 13.0 - - - +
53D LYS* 1.3 83.7 - - - +
55D ASP* 1.3 58.5 + - - +
56D HIS* 4.1 6.1 - - - -
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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) + - + + + + + -
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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