Contacts of the strand formed by residues 97 - 107 (chain B) in PDB entry 3I8E
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 SER 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B LYS 4.2 0.2 - - - +
93B GLN* 3.7 0.3 - - - -
94B SER* 2.7 43.2 + - - -
96B GLU* 1.3 96.9 + - - +
98B ILE* 1.3 63.6 + - - +
99B ASP* 4.2 6.6 + - - +
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Residues in contact with ILE 98 (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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52B VAL 4.8 6.1 - - - +
53B LYS* 3.5 48.7 + - + +
91B TYR* 3.2 32.1 - - + +
92B LYS 3.9 3.1 - - - -
93B GLN* 3.5 25.4 - - + +
96B GLU 4.2 7.6 - - - +
97B SER* 1.3 77.7 + - - +
99B ASP* 1.3 73.6 + - - +
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Residues in contact with ASP 99 (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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53B LYS* 5.3 1.3 - - - +
90B GLU 3.6 1.2 - - - +
91B TYR* 3.6 4.2 - - - -
92B LYS* 2.7 57.2 + - + +
94B SER* 3.7 15.9 + - - -
97B SER* 4.2 7.4 + - - +
98B ILE* 1.3 90.0 - - - +
100B ILE* 1.3 63.2 + - - +
101B ILE* 3.6 10.8 + - + +
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Residues in contact with ILE 100 (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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23B PHE* 5.0 7.2 - - + -
39B LEU* 4.1 4.3 - - + -
41B ILE* 3.8 25.4 - - + -
53B LYS* 4.0 18.1 - - + +
55B VAL* 3.6 41.3 - - + -
89B LEU* 4.0 35.7 - - + -
90B GLU 3.6 5.4 - - - +
91B TYR* 4.3 11.7 - - + -
99B ASP* 1.3 70.8 - - - +
101B ILE* 1.3 60.7 + - - +
102B THR* 4.8 0.2 + - - -
1065B VAL* 4.4 23.1 - - + +
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Residues in contact with ILE 101 (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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89B LEU* 3.2 11.9 - - - +
90B GLU* 2.8 58.6 + - + +
92B LYS* 4.8 26.0 - - + +
99B ASP* 3.6 12.5 + - + +
100B ILE* 1.3 74.4 - - - +
102B THR* 1.3 68.5 + - - +
103B ARG* 4.4 9.6 - - + -
1067B LYS* 6.3 2.2 - - - -
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Residues in contact with THR 102 (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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87B CYS* 3.9 8.3 - - + -
88B ILE 3.5 1.3 - - - +
89B LEU* 4.1 3.1 - - + -
100B ILE 4.8 0.2 + - - -
101B ILE* 1.3 81.5 - - - +
103B ARG* 1.3 64.4 + - - +
104B ALA* 3.2 21.5 + - - +
105B HIS* 4.0 4.3 - - + +
1064B SER 4.4 0.5 + - - -
1065B VAL 2.8 19.9 + - - +
1066B GLY* 3.5 29.8 - - - +
1067B LYS* 3.4 36.7 + - + +
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Residues in contact with ARG 103 (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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72B GLU* 2.8 32.3 + - - +
76B LEU* 4.4 16.5 - - + +
88B ILE* 2.6 26.9 + - + +
90B GLU* 3.4 41.0 + - + +
101B ILE* 3.8 6.0 + - + -
102B THR* 1.3 73.0 - - - +
104B ALA* 1.3 61.0 + - - +
150B LYS* 3.4 29.6 - - - +
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Residues in contact with ALA 104 (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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87B CYS* 3.2 1.7 - - - +
88B ILE* 2.7 39.6 + - + +
102B THR* 3.2 5.5 - - - +
103B ARG* 1.3 80.9 - - - +
105B HIS* 1.3 61.5 + - - +
149B ASN 4.2 3.4 - - - +
150B LYS* 3.4 31.0 - - + +
152B LEU* 4.1 16.8 - - + -
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Residues in contact with HIS 105 (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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86B ALA 3.3 13.9 - - - +
87B CYS* 3.8 1.1 - - + +
102B THR* 4.0 5.1 - - + +
104B ALA* 1.3 76.6 - - - +
106B GLY* 1.3 70.9 + - - +
150B LYS 3.1 11.6 + - - +
151B GLU* 3.0 27.6 - - - -
152B LEU* 3.4 6.5 + - - -
1066B GLY 3.2 20.6 - - - +
1067B LYS* 3.5 41.4 + - + +
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Residues in contact with GLY 106 (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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85B ASN* 5.1 0.9 - - - -
86B ALA* 3.0 28.8 + - - +
105B HIS* 1.3 90.6 - - - +
107B ASN* 1.3 64.5 + - - -
108B VAL* 3.6 6.3 + - - +
151B GLU* 3.7 13.5 - - - -
152B LEU* 4.6 1.4 - - - +
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Residues in contact with ASN 107 (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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83B LYS 3.1 26.7 + - - -
84B TYR* 3.3 17.7 + - - +
85B ASN* 3.9 19.6 - - - +
106B GLY* 1.3 71.9 - - - -
108B VAL* 1.3 60.6 + - - +
109B GLN* 3.1 32.3 + - - +
1072B PHE* 4.2 8.6 - - + -
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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