Contacts of the strand formed by residues 67 - 75 (chain B) in PDB entry 3HIG
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 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B GLU 5.3 0.8 + - - -
54B LEU* 2.7 32.2 + - - +
55B ARG* 3.9 14.3 + - - +
56B LEU* 3.4 7.9 - - + -
57B GLN* 2.8 28.8 + - - +
66B LYS* 1.3 72.9 - - - +
68B THR* 1.3 62.8 + - - +
101B ILE* 4.9 0.2 - - + -
102B PHE 3.1 6.7 - - - +
103B PHE* 3.2 26.6 - - + +
104B GLY 3.0 6.9 + - - -
105B ASP* 2.8 43.6 + - - +
106B GLN* 5.0 2.4 + - - -
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Residues in contact with THR 68 (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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56B LEU* 3.9 4.6 - - - +
57B GLN 2.9 22.5 + - - -
59B SER* 3.4 19.8 + - - -
66B LYS* 4.1 27.8 - - + +
67B ASN* 1.3 75.6 - - - +
69B VAL* 1.3 70.0 + - - +
70B PHE* 3.4 4.3 + - + +
101B ILE* 3.4 6.3 - - - +
102B PHE* 2.9 55.2 + - + +
403B TYR* 5.4 0.5 + - - -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B HIS* 4.6 8.3 - - + -
48B LEU* 3.9 25.8 - - + -
49B TRP* 4.8 3.1 - - - +
56B LEU* 3.8 30.2 - - + +
57B GLN 4.8 0.6 + - - -
59B SER* 5.2 3.3 - - - -
68B THR* 1.3 77.8 + - - +
70B PHE* 1.3 59.9 + - - +
71B LEU 4.1 3.4 - - - +
72B ILE* 3.7 33.7 - - + -
99B ALA* 4.6 4.0 - - + -
100B VAL 3.7 9.6 - - - +
101B ILE* 4.4 7.6 - - + +
403B TYR* 3.1 30.6 + - + +
406B ALA 4.7 2.9 + - - +
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Residues in contact with PHE 70 (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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59B SER* 6.3 1.1 - - - -
68B THR* 3.4 6.3 + - + +
69B VAL* 1.3 74.3 - - - +
71B LEU* 1.3 64.6 + - + +
100B VAL* 2.8 17.9 + - + +
102B PHE* 3.4 49.6 - + + -
142B PRO* 3.6 29.4 - - + -
143B ILE 4.1 9.6 - - - -
144B SER* 4.3 4.5 - - - -
403B TYR* 4.1 3.0 - - - +
404B TYR* 3.5 44.5 + + - -
405B ASP* 2.8 61.4 + - + +
637B ILE* 4.8 8.7 - - + -
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Residues in contact with LEU 71 (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 VAL* 3.6 1.1 - - - +
70B PHE* 1.3 89.1 - - + +
72B ILE* 1.3 83.8 + - - +
73B GLU* 4.0 20.4 - - + +
98B ARG* 3.8 24.7 - - - +
99B ALA* 3.4 4.0 - - - -
100B VAL* 2.9 52.9 + - + +
330B SER* 4.1 12.6 - - - -
331B SER* 4.4 8.7 - - - +
403B TYR* 3.4 13.7 - - - +
404B TYR* 4.3 15.3 - - + -
637B ILE* 4.5 11.2 - - + -
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Residues in contact with ILE 72 (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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36B LEU* 3.8 11.7 - - + -
41B LEU* 3.5 45.6 - - + +
44B VAL* 3.8 34.3 - - + -
45B HIS* 4.1 15.3 - - + +
48B LEU* 4.9 0.2 - - + -
69B VAL* 3.7 16.8 - - + -
71B LEU* 1.3 80.3 - - - +
73B GLU* 1.3 64.9 + - - +
97B ALA* 4.0 3.1 - - + -
98B ARG 3.2 9.6 - - - +
99B ALA* 4.6 2.2 - - + -
330B SER* 4.8 3.1 + - - -
403B TYR* 3.2 44.6 + - + +
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Residues in contact with GLU 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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36B LEU* 3.8 11.4 - - - -
41B LEU* 5.0 0.4 - - - -
71B LEU* 4.0 8.2 - - + +
72B ILE* 1.3 76.2 - - - +
74B MET* 1.3 65.0 + - - +
97B ALA* 3.4 2.8 - - - -
98B ARG* 2.7 71.4 + - - -
327B ARG* 4.5 4.7 - - - +
329B ARG* 3.4 18.4 + - - +
330B SER* 3.2 20.4 + - - +
331B SER* 2.8 47.2 + - - -
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Residues in contact with MET 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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32B VAL 3.7 11.2 - - - +
33B PHE 3.3 25.1 - - - +
34B SER 3.3 28.5 - - - +
35B ASP* 4.4 0.4 - - - +
36B LEU* 3.7 24.7 - - + +
73B GLU* 1.3 83.1 - - - +
75B LEU* 1.3 62.0 + - - +
76B LEU* 3.4 31.4 - - + -
77B PRO* 4.8 2.0 - - - -
95B ARG* 3.6 16.8 - - + +
96B GLU 3.7 12.1 - - - +
98B ARG* 5.0 0.5 - - - +
327B ARG* 3.3 44.0 + - - +
329B ARG* 5.2 1.9 + - - -
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Residues in contact with LEU 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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73B GLU 3.5 0.8 + - - -
74B MET* 1.3 75.1 - - - +
76B LEU* 1.3 72.9 + - - +
77B PRO* 3.4 5.2 - - - +
94B VAL 5.5 0.3 - - - +
96B GLU* 3.1 48.4 + - - +
97B ALA 4.0 2.9 - - - +
98B ARG* 3.8 29.6 - - + +
115B ALA* 3.8 25.6 - - + -
128B LEU* 4.4 17.0 - - + -
329B ARG* 6.3 0.9 - - - +
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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