Contacts of the helix formed by residues 61 - 80 (chain B) in PDB entry 3H1S
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 ASN 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B SER* 1.3 76.9 - - - +
62B GLY* 1.3 73.8 + - - +
63B GLY 3.5 0.2 + - - -
64B ILE* 3.5 8.8 + - - +
65B PHE* 3.1 18.1 + - - -
301B GOL 3.7 13.5 - - - +
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Residues in contact with GLY 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASN* 1.3 81.8 + - - +
63B GLY* 1.3 63.1 + - - -
65B PHE* 3.6 2.8 - - - +
66B ASN* 3.1 31.2 + - - -
301B GOL 4.8 1.0 + - - -
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Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.6 16.1 - - - +
61B ASN 3.5 0.2 + - - -
62B GLY* 1.3 70.7 - - - -
64B ILE* 1.3 65.8 + - - +
66B ASN* 3.4 8.0 + - - +
67B ASN* 2.9 32.1 + - - +
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.0 4.6 - - + +
42B LEU* 3.8 40.5 - - + +
43B VAL* 4.0 18.2 - - + -
46B THR* 4.4 11.7 - - + +
48B HIS* 3.9 20.0 - - + -
56B ILE* 3.5 28.5 - - + -
60B SER* 3.6 9.4 - - - -
61B ASN 3.5 7.1 + - - +
62B GLY 3.3 0.6 - - - -
63B GLY* 1.3 75.9 - - - +
65B PHE* 1.3 60.0 + - - +
67B ASN* 3.9 0.4 - - - -
68B ALA* 2.8 32.4 + - - +
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 3.3 30.5 - - + -
60B SER* 3.1 20.7 + - - +
61B ASN* 3.1 29.6 + - - -
62B GLY 3.6 1.8 - - - +
64B ILE* 1.3 76.6 - - - +
66B ASN* 1.3 77.4 + - - +
68B ALA* 4.5 0.9 - - - -
69B ALA* 2.8 52.0 + - + +
141B ALA* 3.9 20.4 - - + -
142B GLY* 4.3 9.9 - - - -
143B CYS 4.5 1.3 - - - -
146B THR* 3.8 17.7 - - + -
301B GOL 3.8 33.4 - - - -
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Residues in contact with ASN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 3.6 53.3 - - + +
35B TYR* 4.6 0.2 - - - -
62B GLY 3.1 19.7 + - - +
63B GLY* 3.8 8.0 - - - +
64B ILE 3.3 0.4 - - - -
65B PHE* 1.3 94.3 - - - +
67B ASN* 1.3 58.8 + - - +
70B GLN* 3.1 35.9 + - - +
140B ASN* 5.7 0.2 - - - +
141B ALA* 3.4 9.6 + - - +
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Residues in contact with ASN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 5.5 2.4 - - - -
35B TYR* 3.4 39.4 - - - +
38B ASN* 3.3 33.5 + - - +
39B LEU* 3.9 13.9 - - - +
42B LEU* 3.4 14.9 - - + +
63B GLY* 2.9 23.5 + - - +
64B ILE 4.1 0.9 - - - +
66B ASN* 1.3 76.7 - - - +
68B ALA* 1.3 65.4 + - - +
70B GLN* 3.3 2.1 + - - +
71B VAL* 2.9 30.2 + - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.8 15.3 - - + +
53B LEU* 3.6 19.4 - - + +
56B ILE* 3.6 27.8 - - + -
57B VAL* 3.8 11.2 - - + +
64B ILE 2.8 22.3 + - - +
65B PHE* 3.9 3.8 - - - +
67B ASN* 1.3 72.9 - - - +
69B ALA* 1.3 62.1 + - - +
71B VAL* 3.2 4.9 + - - +
72B PHE* 3.1 19.9 + - - +
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B VAL* 3.8 17.0 - - + +
65B PHE* 2.8 44.1 + - + +
68B ALA* 1.3 71.3 - - - +
70B GLN* 1.3 58.0 + - - +
72B PHE* 3.2 2.8 + - - +
73B ASN* 2.8 36.1 + - - +
141B ALA* 3.0 26.2 - - + +
143B CYS* 4.3 3.1 - - + -
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 4.0 3.8 - - + -
35B TYR* 3.1 50.9 + - + -
66B ASN 3.1 27.1 + - - +
67B ASN 3.8 0.2 - - - +
68B ALA 3.3 0.2 - - - -
69B ALA* 1.3 76.7 - - - +
71B VAL* 1.3 61.7 + - - +
73B ASN* 3.3 8.6 + - - +
74B HIS* 2.8 46.9 + - - +
122B TRP* 3.0 26.1 + - - -
140B ASN 4.0 0.2 - - - -
141B ALA* 3.5 16.3 - - + -
158B TRP* 3.3 27.1 - - - +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 5.6 4.7 - - + -
4B GLU 5.3 4.9 - - - +
6B PRO* 5.7 0.9 - - + -
32B HIS* 3.2 14.7 - - + -
35B TYR* 3.6 8.3 - - + +
36B VAL* 3.6 48.5 - - + +
39B LEU* 4.2 11.7 - - + -
53B LEU* 3.7 22.2 - - + -
67B ASN 2.9 18.6 + - - +
68B ALA 3.2 6.9 + - - +
70B GLN* 1.3 73.9 - - - +
72B PHE* 1.3 63.9 + - - +
75B THR* 3.1 30.6 + - - +
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.8 21.3 - - + -
54B GLU* 4.0 23.8 - - + -
57B VAL* 4.1 9.0 - - + -
68B ALA 3.1 12.3 + - - +
69B ALA 3.5 6.3 - - - +
71B VAL* 1.3 77.7 - - - +
73B ASN* 1.3 70.4 + - - +
75B THR* 3.3 5.3 + - - -
76B PHE* 2.9 46.8 + + + +
124B TRP* 4.7 2.5 - + - -
143B CYS* 3.6 21.5 - - - -
145B LEU* 3.7 26.2 - - + -
151B PRO* 4.1 23.8 - - + -
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ALA 2.8 23.1 + - - +
70B GLN* 3.3 16.4 + - - +
72B PHE* 1.3 74.9 - - - +
74B HIS* 1.3 57.8 + - - +
76B PHE* 3.4 3.4 + - - +
77B TYR* 2.9 28.6 + - - +
122B TRP* 3.4 34.9 - - + +
124B TRP* 3.2 28.4 - - + -
141B ALA 3.1 25.9 + - - -
142B GLY 3.5 5.9 + - - -
143B CYS* 3.4 16.6 - - - +
154B THR* 4.1 1.0 - - - +
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Residues in contact with HIS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B HIS* 3.1 22.3 + + - -
31B HIS* 5.2 0.2 - - - +
32B HIS* 3.5 31.0 - + + +
35B TYR* 3.5 28.2 - + - -
70B GLN* 2.8 36.3 + - - +
73B ASN* 1.3 74.8 - - - +
75B THR* 1.3 65.1 + - - +
77B TYR* 3.2 7.1 + + - +
78B TRP* 3.0 38.4 + + - +
122B TRP* 3.5 19.1 - + - -
156B ASP* 3.4 3.7 + - - -
160B HIS* 3.8 0.8 + - - -
1001B FE 2.1 32.0 - - - -
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Residues in contact with THR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PRO* 3.3 27.8 - - + +
32B HIS* 3.2 15.8 + - - -
53B LEU* 6.2 0.9 - - - -
71B VAL* 3.1 22.4 + - - +
72B PHE* 3.7 5.8 - - - -
74B HIS* 1.3 77.2 - - - +
76B PHE* 1.3 64.9 + - - +
78B TRP* 3.4 7.3 + - - +
79B ASN* 3.2 39.0 + - - +
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 2.9 36.5 + + + +
73B ASN* 3.5 8.1 - - - +
75B THR* 1.3 76.4 - - - +
77B TYR* 1.3 62.4 + - - +
79B ASN* 3.1 11.8 + - - +
80B CYS* 3.1 44.3 + - - -
124B TRP* 4.0 8.5 - + + -
151B PRO* 3.3 44.2 - - + -
152B LEU* 3.6 5.6 - - - -
153B LEU* 3.7 17.0 - - - -
154B THR* 3.7 13.5 - - + -
185B PHE* 3.6 29.4 - + - -
189B GLN* 4.3 8.3 - - + -
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Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 3.7 18.4 - - - +
27B HIS* 3.6 19.8 + + - -
73B ASN 2.9 20.0 + - - +
74B HIS* 3.4 6.7 - + - +
76B PHE* 1.3 72.6 - - - +
78B TRP* 1.3 100.3 + + - +
80B CYS* 3.0 19.0 + - - +
81B LEU* 3.4 31.7 - - + +
122B TRP* 4.0 7.2 - + + -
154B THR* 3.7 30.0 - - + +
155B PHE* 4.4 2.2 - - - -
156B ASP* 3.6 27.4 - - + -
161B ALA* 4.3 5.2 + - - +
173B TYR* 2.8 24.9 + - - -
177B LEU* 4.3 3.7 - - + +
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Residues in contact with TRP 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PRO* 5.3 3.4 - - + -
8B LEU* 3.7 19.3 - - + -
9B PRO* 3.9 10.6 - - + +
10B TYR* 2.7 38.6 + - - +
19B ILE* 5.3 1.8 - - + -
24B ILE* 3.4 32.1 - - + -
27B HIS* 3.5 36.3 - + + -
28B TYR* 3.6 38.0 - + + -
32B HIS* 3.1 30.9 - + - -
74B HIS* 3.0 31.3 + + - +
75B THR* 4.0 6.3 - - - +
76B PHE 3.4 0.2 - - - -
77B TYR* 1.3 98.4 - + - +
79B ASN* 1.3 58.5 + - - +
81B LEU* 3.2 22.5 + - + +
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Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 3.7 20.1 - - - +
75B THR* 3.2 30.3 + - - +
76B PHE* 3.1 10.0 + - - +
78B TRP* 1.3 77.0 - - - +
80B CYS* 1.3 55.5 + - - +
81B LEU 3.2 3.8 - - - -
182B ASN* 3.4 14.3 + - - +
185B PHE* 3.3 51.3 - - + +
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Residues in contact with CYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PHE* 3.1 44.4 + - - -
77B TYR 3.0 12.2 + - - +
79B ASN* 1.3 74.9 - - - +
81B LEU* 1.3 58.6 + - + +
152B LEU 4.3 0.2 - - - -
153B LEU* 3.7 21.4 - - + +
154B THR 3.5 23.1 - - - +
181B VAL* 3.4 10.7 - - - +
182B ASN* 2.7 30.1 + - - -
185B PHE* 3.8 13.2 - - - -
186B VAL* 5.0 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
------------------------------------------------------------
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