Contacts of the strand formed by residues 67 - 75 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A GLU 5.3 0.6 + - - -
54A LEU* 2.8 30.9 + - - +
55A ARG* 3.5 18.6 + - - +
56A LEU* 3.4 7.5 - - + -
57A GLN* 2.7 34.3 + - - +
66A LYS* 1.3 73.2 - - - +
68A THR* 1.3 58.0 + - - +
101A ILE* 5.1 0.2 - - + -
102A PHE 3.2 4.3 - - - +
103A PHE* 3.3 26.2 - - + +
104A GLY 3.2 6.4 + - - -
105A ASP* 2.9 43.0 + - - +
106A GLN* 4.7 3.1 + - - +
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.8 6.8 - - - +
57A GLN 3.1 18.4 + - - -
59A SER* 3.4 21.6 + - - -
66A LYS* 4.1 24.2 - - + +
67A ASN* 1.3 75.5 - - - +
69A VAL* 1.3 70.6 + - - +
70A PHE* 3.5 5.1 + - + +
101A ILE* 3.4 2.1 - - - +
102A PHE* 2.8 60.6 + - + -
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A HIS* 5.0 3.1 - - + -
48A LEU* 3.8 26.2 - - + -
49A TRP* 5.1 5.8 - - - +
56A LEU* 3.7 31.8 - - + +
57A GLN 4.8 0.8 + - - -
59A SER* 5.1 3.1 - - - -
68A THR* 1.3 78.9 + - - +
70A PHE* 1.3 63.3 + - - +
71A LEU 4.0 3.1 - - - +
72A ILE* 3.7 34.8 - - + -
99A ALA* 4.7 2.2 - - + -
100A VAL 3.6 10.8 - - - +
101A ILE* 4.1 7.2 - - + +
403A TYR* 3.4 25.2 + - + +
406A ALA 4.5 3.6 + - - +
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER* 6.2 1.1 - - - -
68A THR* 3.5 6.7 + - + +
69A VAL* 1.3 74.4 - - - +
71A LEU* 1.3 69.0 + - + +
100A VAL* 2.8 14.9 + - + +
102A PHE* 3.5 51.1 - + + -
142A PRO* 3.7 26.2 - - + -
143A ILE 4.2 9.4 - - - -
144A SER* 4.3 4.3 - - - -
403A TYR* 4.0 3.1 - - - +
404A TYR* 3.5 48.2 - + - -
405A ASP* 2.8 60.5 + - + +
637A ILE* 4.9 5.8 - - + -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 3.6 1.3 - - - +
70A PHE* 1.3 92.9 - - + +
72A ILE* 1.3 77.9 + - - +
73A GLU* 4.0 21.3 - - + +
98A ARG* 3.8 30.5 - - - +
99A ALA* 3.3 4.7 - - - -
100A VAL* 2.8 45.9 + - + +
330A SER* 4.0 13.7 - - - -
331A SER* 4.6 6.7 - - - +
403A TYR* 3.4 17.5 - - - +
404A TYR* 4.1 15.7 - - + -
637A ILE* 4.5 10.8 - - + -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.0 10.5 - - + -
41A LEU* 3.6 33.0 - - + +
44A VAL* 3.7 36.8 - - + -
45A HIS* 4.0 26.5 - - + +
48A LEU* 4.7 1.3 - - + -
69A VAL* 3.7 20.0 - - + -
71A LEU* 1.3 80.9 - - - +
73A GLU* 1.3 67.2 + - - +
97A ALA* 4.0 2.5 - - + -
98A ARG 3.2 10.3 - - - +
99A ALA* 4.6 2.9 - - + -
330A SER* 4.7 2.1 + - - -
403A TYR* 3.2 38.8 + - + +
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.6 11.2 - - - -
41A LEU* 4.9 0.4 - - - -
71A LEU* 4.0 8.3 - - + +
72A ILE* 1.3 76.5 - - - +
74A MET* 1.3 66.3 + - - +
97A ALA* 3.3 2.3 - - - -
98A ARG* 2.6 67.3 + - - -
327A ARG* 4.6 4.9 - - - +
329A ARG* 3.5 19.2 + - - -
330A SER* 3.2 20.5 + - - +
331A SER* 2.8 47.1 + - - -
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Residues in contact with MET 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL 3.8 11.4 - - - +
33A PHE 3.3 32.5 - - - +
34A SER 3.4 20.4 - - - +
35A ASP* 4.4 0.6 + - - -
36A LEU* 3.5 28.5 - - + +
73A GLU* 1.3 83.7 - - - +
75A LEU* 1.3 78.6 + - - +
76A LEU* 3.5 16.2 - - + -
77A PRO* 4.8 1.1 - - - -
95A ARG* 3.7 14.8 - - + +
96A GLU 3.8 12.8 - - - +
98A ARG* 4.9 0.7 - - - +
327A ARG* 3.3 45.1 + - - +
329A ARG* 5.2 2.3 + - - -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLU 3.5 0.6 + - - -
74A MET* 1.3 77.1 - - - +
76A LEU* 1.3 74.4 + - - +
77A PRO* 3.5 4.9 - - - +
94A VAL 5.5 0.3 - - - +
95A ARG* 5.7 0.2 - - - -
96A GLU* 3.0 44.8 + - + +
97A ALA 4.0 0.9 - - - +
98A ARG* 3.8 18.8 - - + +
115A ALA* 3.5 33.0 - - + -
126A ARG* 4.0 7.0 - - - +
128A LEU* 4.1 31.0 - - + -
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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