Contacts of the helix formed by residues 41 - 55 (chain H) in PDB entry 2H4C
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 THR 41 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H TYR* 3.8 25.2 + - + -
25H TYR* 3.3 24.5 - - + -
29H CYS* 3.6 11.6 - - - -
39H ASP* 3.1 16.8 + - - -
40H ALA* 1.3 73.9 - - - +
42H ASP* 1.3 56.8 + - - +
43H ARG 2.8 3.6 - - - -
44H CYS* 2.4 44.1 + - - +
45H CYS 3.4 2.1 + - - -
106H PHE* 4.0 7.3 + - + -
109H ASN* 4.1 18.5 + - - +
112H THR* 4.5 0.2 + - - -
113H TYR* 4.1 13.0 - - - -
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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
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25H TYR* 4.3 0.4 - - + -
26H GLY* 3.9 11.2 - - - -
27H CYS* 3.0 26.9 + - - +
28H TYR* 2.7 25.8 + - - -
29H CYS* 2.9 22.0 + - - -
37H PRO* 3.1 9.3 - - - +
38H LYS 2.9 29.1 + - - +
39H ASP* 2.8 19.8 + - - +
41H THR* 1.3 73.4 - - - +
43H ARG* 1.3 56.4 + - - +
45H CYS* 3.1 3.2 + - - +
46H PHE* 2.9 27.9 + - - +
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Residues in contact with ARG 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H PRO* 3.6 29.8 + - + +
38H LYS 5.4 0.4 - - - -
39H ASP* 2.9 35.1 + - - +
40H ALA* 3.3 18.7 - - - +
41H THR 2.7 4.0 + - - -
42H ASP* 1.3 74.3 - - - +
44H CYS* 1.3 57.3 + - - -
46H PHE* 4.2 2.9 - - + +
47H VAL* 3.3 24.9 + - + +
105H CYS* 5.2 0.9 - - - -
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Residues in contact with CYS 44 (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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40H ALA 2.8 22.9 - - - -
41H THR* 2.4 29.4 + - - +
43H ARG* 1.3 71.4 - - - +
45H CYS* 1.3 65.0 + - - +
47H VAL* 3.4 8.6 + - - +
48H HIS* 3.3 17.7 + - - +
102H ALA* 4.5 11.9 - - - +
105H CYS* 2.6 48.5 - - + -
106H PHE* 4.0 23.3 - - + -
109H ASN* 4.0 4.0 - - - -
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Residues in contact with CYS 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H PHE* 6.2 0.9 - - - -
22H TYR* 5.1 1.1 - - - -
28H TYR* 3.9 2.5 - - - +
29H CYS* 2.0 65.3 - - - +
42H ASP 3.1 1.9 + - - +
44H CYS* 1.3 78.4 - - - +
46H PHE* 1.3 60.4 + - - +
48H HIS* 2.8 31.4 + - - +
49H ASP* 3.2 13.2 + - - +
102H ALA* 6.1 0.4 - - - -
106H PHE* 3.3 28.5 - - - -
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Residues in contact with PHE 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G MET* 4.8 2.9 - - + -
28H TYR* 3.3 48.6 - + + +
37H PRO* 3.6 29.8 - - + -
42H ASP 2.9 9.2 + - - +
43H ARG* 4.5 3.8 - - + +
44H CYS 3.5 0.2 - - - -
45H CYS* 1.3 76.1 - - - +
47H VAL* 1.3 72.2 - - + +
49H ASP* 3.6 4.7 + - - +
50H CYS* 3.5 34.1 + - - -
131H ASP* 3.6 31.0 - - + -
132H GLN 3.0 27.8 - - - -
133H CYS* 4.4 3.8 - - - -
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Residues in contact with VAL 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H ARG* 3.3 20.2 - - + +
44H CYS* 3.4 10.7 + - - +
45H CYS 3.1 0.4 - - - -
46H PHE* 1.3 88.0 - - + +
48H HIS* 1.3 61.1 + - - +
50H CYS* 3.3 8.3 + - + +
51H CYS* 2.9 29.9 + - + +
101H VAL* 6.4 1.8 - - + -
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Residues in contact with HIS 48 (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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69G LYS* 5.8 2.4 + - - -
2H LEU* 5.4 0.7 - - + -
5H PHE* 3.2 43.2 - + - -
44H CYS 3.3 9.5 + - - +
45H CYS* 2.8 18.1 + - - +
47H VAL* 1.3 81.2 - - - +
49H ASP* 1.3 59.5 + - - +
51H CYS* 3.5 6.0 - - - +
52H TYR* 2.8 68.9 + + - +
98H CYS* 3.8 11.0 - - + -
99H ASP* 2.9 23.3 + - - -
102H ALA* 3.6 16.4 - - + -
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Residues in contact with ASP 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ASN* 4.1 6.4 + - - +
69G LYS* 3.6 35.3 + - + +
70G MET* 3.3 27.6 - - + +
28H TYR* 3.2 36.4 - - - +
45H CYS* 3.2 13.5 + - - +
46H PHE* 3.8 2.9 - - - +
47H VAL 3.3 0.2 - - - -
48H HIS* 1.3 78.4 + - - +
50H CYS* 1.3 71.6 + - - +
52H TYR* 3.5 8.0 + - - +
53H ALA* 3.2 17.8 + - - +
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Residues in contact with CYS 50 (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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70G MET* 4.9 0.4 - - - -
46H PHE* 3.5 29.8 + - - -
47H VAL* 3.3 9.5 + - - +
49H ASP* 1.3 76.1 - - - +
51H CYS* 1.3 69.5 + - - +
53H ALA* 2.5 25.0 + - - +
54H ARG* 3.2 16.1 + - - +
133H CYS* 2.0 61.0 - - + +
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Residues in contact with CYS 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H VAL* 2.9 14.6 + - + +
48H HIS* 3.5 9.6 - - - +
50H CYS* 1.3 77.0 - - - +
52H TYR* 1.3 59.8 + - - +
53H ALA 2.6 1.4 + - - -
54H ARG* 2.4 49.1 + - - +
55H VAL* 3.3 13.1 + - - -
98H CYS* 2.0 52.9 - - + -
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Residues in contact with TYR 52 (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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61G ASN* 5.6 1.6 - - - +
69G LYS* 6.5 0.7 - - + -
1H ASN 4.7 2.1 + - - -
2H LEU* 4.2 22.4 - - + +
5H PHE* 4.3 0.7 - - - +
48H HIS* 2.8 45.5 + + - +
49H ASP* 3.7 9.0 - - - +
50H CYS 3.1 0.2 + - - -
51H CYS* 1.3 82.1 - - - +
53H ALA* 1.3 59.2 + - - +
55H VAL* 3.9 8.7 - - + +
68H PRO* 3.5 60.8 + - + +
69H LYS* 4.6 3.8 - - + -
95H VAL* 4.4 12.3 - - + +
98H CYS* 4.7 0.9 - - + -
99H ASP* 2.9 40.8 + - - -
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Residues in contact with ALA 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G ASN* 4.1 29.6 + - + +
70G MET* 6.0 0.2 - - - -
49H ASP 3.2 10.2 + - - +
50H CYS* 2.5 22.2 + - - +
52H TYR* 1.3 71.3 - - - +
54H ARG* 1.3 65.0 + - + +
55H VAL 3.8 4.7 - - - +
133H CYS* 5.9 1.6 - - - -
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Residues in contact with ARG 54 (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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50H CYS* 3.5 16.6 + - - +
51H CYS* 2.4 38.7 + - - +
53H ALA* 1.3 69.3 - - - +
55H VAL* 1.3 68.5 + - + +
56H LYS* 2.9 33.6 - - - +
133H CYS* 3.1 53.1 + - - +
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Residues in contact with VAL 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H CYS* 4.0 24.2 - - - +
52H TYR* 3.9 15.4 - - + +
53H ALA 3.5 7.0 - - - +
54H ARG* 1.3 82.1 - - + +
56H LYS* 1.3 60.4 + - - +
59H CYS* 3.3 24.9 - - - +
68H PRO* 4.1 4.6 - - + +
91H CYS* 3.2 27.8 - - + -
94H ALA* 4.0 22.9 - - + -
95H VAL* 3.9 17.0 - - + +
98H CYS* 5.1 0.2 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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