Contacts of the strand formed by residues 95 - 102 (chain A) in PDB entry 3H1I
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TRP 3.7 0.9 - - - -
41A ILE* 2.8 33.3 + - - +
43A ALA* 2.6 28.9 + - - -
44A GLY* 4.0 0.3 - - - -
56A GLY 4.6 4.9 + - - +
89A TYR* 2.7 27.8 - - - +
90A THR* 3.5 23.5 + - - +
94A GLN* 1.3 77.8 - - - +
96A ALA* 1.3 71.0 + - - +
97A PHE* 3.6 26.5 - - + -
185A TYR* 4.0 7.3 + - - -
190A PHE* 5.1 5.8 - - + -
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Residues in contact with ALA 96 (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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39A VAL 3.3 11.0 - - - +
40A TRP* 3.0 40.8 - - + +
41A ILE 4.5 1.1 - - - +
88A GLY* 3.2 3.2 - - - -
89A TYR* 2.9 40.8 + - + +
95A THR* 1.3 85.2 - - - +
97A PHE* 1.3 69.0 - - - +
98A TYR* 4.2 1.8 - - + -
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Residues in contact with PHE 97 (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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38A GLY* 3.3 1.2 - - - -
39A VAL* 3.0 38.7 + - + +
41A ILE* 4.1 22.7 - - + -
59A VAL* 4.6 2.2 - - + -
60A GLU* 4.0 26.2 - - + -
63A ALA* 3.2 30.7 - - + -
64A PHE* 3.9 20.6 - + - -
86A PHE* 3.8 18.8 - - + -
87A ASN 4.1 4.0 - - - -
88A GLY* 5.1 2.0 - - - -
95A THR* 3.6 29.2 - - + -
96A ALA* 1.3 77.6 - - - +
98A TYR* 1.3 60.2 + - - +
113A LEU* 3.9 5.9 - - + +
116A VAL* 5.2 6.1 - - + -
117A VAL* 5.0 6.3 - - + -
190A PHE* 4.2 14.8 - + - -
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Residues in contact with TYR 98 (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 THR* 4.0 15.0 - - + -
37A VAL 3.4 8.5 - - - +
38A GLY* 3.5 15.5 - - - -
40A TRP* 3.9 30.5 - + + -
85A HIS 3.8 1.3 - - - +
86A PHE* 3.1 9.6 - - - -
87A ASN* 2.5 68.2 + - + +
88A GLY* 3.9 12.3 - - - -
89A TYR* 4.5 18.4 - + - -
96A ALA* 4.7 4.0 - - + -
97A PHE* 1.3 75.7 - - - +
99A ILE* 1.3 67.7 + - - +
100A LYS* 4.9 7.6 - - + -
113A LEU* 4.4 0.7 - - - -
373A THR* 3.7 26.0 - - + +
377A GLU* 5.5 0.4 - - + -
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Residues in contact with ILE 99 (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 THR* 3.0 8.9 - - - +
37A VAL* 2.7 39.6 + - - +
79A VAL* 5.3 4.5 - - + -
84A ALA* 3.4 30.7 - - + -
85A HIS 3.2 13.2 - - - +
86A PHE* 3.2 51.6 - - + +
98A TYR* 1.3 74.2 - - - +
100A LYS* 1.3 64.9 + - - +
101A ALA* 4.0 4.5 + - + +
109A VAL* 3.9 25.5 - - + +
112A LEU* 4.6 16.2 - - + -
113A LEU* 3.8 8.1 - - + -
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Residues in contact with LYS 100 (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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35A CYS 3.4 6.8 + - - +
36A THR* 3.1 12.8 + - + +
84A ALA* 3.1 5.4 - - - -
85A HIS* 2.8 52.8 + - + +
98A TYR* 4.9 8.3 - - + -
99A ILE* 1.3 72.7 - - - +
101A ALA* 1.3 60.1 + - - +
372A THR* 3.0 27.9 + - - -
373A THR* 3.2 20.1 + - + +
370B MET* 3.9 32.1 - - - +
373B GLU* 3.0 20.3 + - - -
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Residues in contact with ALA 101 (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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34A THR* 4.0 5.1 + - - -
35A CYS* 2.8 45.5 + - - -
82A MET 6.0 0.2 - - - +
83A GLY 5.1 1.3 - - - -
84A ALA* 3.5 23.1 - - + +
99A ILE* 4.0 4.3 + - + +
100A LYS* 1.3 76.3 - - - +
102A LEU* 1.3 60.9 + - + +
105A ASP* 4.5 7.0 - - - +
109A VAL* 4.1 23.8 - - + -
370B MET* 5.1 3.6 - - - -
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Residues in contact with LEU 102 (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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33A PRO 4.0 7.2 - - - +
34A THR* 4.1 7.0 - - - +
35A CYS* 4.0 1.4 - - - -
82A MET 3.8 16.8 - - - +
83A GLY 5.6 1.3 - - - +
101A ALA* 1.3 75.1 - - + +
103A SER* 1.3 54.9 + - - +
104A LYS* 2.7 43.8 + - + +
105A ASP* 3.0 35.2 + - - +
106A MET 3.7 4.9 + - - -
362B ASN* 5.3 8.3 - - + +
365B LYS* 5.4 3.6 - - + -
366B ALA* 4.1 32.5 - - + +
369B LEU* 4.9 14.4 - - + -
370B MET* 6.4 0.7 - - + -
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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