Contacts of the strand formed by residues 94 - 103 (chain B) in PDB entry 3ABD
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 PRO 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B VAL* 3.9 15.5 - - + -
87B ILE 3.5 7.4 - - - +
88B LEU* 3.6 7.4 - - + -
92B HIS 3.6 3.4 - - - +
93B ARG* 1.3 81.7 - - + +
95B VAL* 1.3 55.3 + - - +
97B LYS* 4.2 8.5 - - + -
177B GLN 3.6 15.9 - - - +
178B ASP 3.5 24.0 - - - +
179B VAL 4.3 1.8 - - - +
180B HIS 3.7 20.2 - - - +
181B MET* 3.1 18.1 - - + +
206B ARG* 2.8 35.3 + - - +
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Residues in contact with VAL 95 (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 ILE* 2.8 36.2 + - + +
89B ASP* 4.0 21.8 - - + +
93B ARG* 3.1 14.1 + - - +
94B PRO* 1.3 75.2 - - - +
96B GLU* 1.3 63.4 + - - +
140B ASN* 3.8 18.2 - - - +
141B PRO* 4.5 5.6 - - + -
144B CYS* 4.1 11.7 - - - -
181B MET* 3.5 6.1 - - - -
205B GLU* 3.7 0.2 - - - -
206B ARG* 2.9 35.3 + - - +
209B LYS* 3.7 25.7 - - + -
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Residues in contact with GLU 96 (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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34B ARG* 2.8 43.5 + - - +
85B VAL 4.0 0.6 - - - +
86B VAL* 3.5 1.2 - - - +
87B ILE* 2.9 34.9 + - + +
95B VAL* 1.3 86.8 + - + +
97B LYS* 1.3 68.1 + - - +
98B PHE* 3.7 12.8 - - + -
137B LEU* 3.7 14.8 - - - +
140B ASN* 3.1 25.3 + - - +
203B VAL* 4.6 2.9 - - + -
204B GLU 3.2 9.2 - - - +
205B GLU* 4.4 6.7 - - + -
209B LYS* 2.7 23.0 + - - +
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Residues in contact with LYS 97 (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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84B VAL* 3.8 16.8 - - + -
85B VAL 3.5 4.5 - - - -
86B VAL* 4.2 17.5 - - + -
94B PRO* 4.2 15.3 - - - -
96B GLU* 1.3 78.7 - - - +
98B PHE* 1.3 64.3 + - - +
99B VAL* 3.6 8.8 + - + +
149B LEU* 5.6 1.5 - - + +
178B ASP 4.9 0.2 - - - -
179B VAL* 2.5 44.8 + - - +
181B MET* 4.4 18.1 - - + +
202B TYR 3.6 1.0 - - - +
203B VAL* 3.1 6.4 - - - +
204B GLU* 2.8 58.7 + - + +
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Residues in contact with PHE 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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30B ILE* 3.7 50.9 - - + -
34B ARG* 3.8 24.2 - - + -
84B VAL* 3.3 3.7 - - - -
85B VAL* 2.9 40.8 + - + +
87B ILE* 4.0 6.7 - - + -
96B GLU* 3.7 22.9 - - + -
97B LYS* 1.3 73.9 - - - +
99B VAL* 1.3 62.1 + - - +
100B PHE* 3.7 9.5 - - + -
130B ILE* 5.1 4.3 - - + -
133B CYS* 4.0 14.4 - - - -
137B LEU* 4.1 9.0 - - + -
189B LEU* 4.7 4.9 - - + -
201B LEU* 4.2 9.9 - - + -
202B TYR 3.7 2.9 - - - -
203B VAL* 3.3 28.3 - - + -
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Residues in contact with VAL 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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82B LYS* 3.9 25.1 - - + +
83B VAL 4.0 2.2 - - - -
84B VAL* 4.0 20.2 - - + -
97B LYS* 4.0 17.9 - - + +
98B PHE* 1.3 75.4 - - - +
100B PHE* 1.3 62.2 + - - +
101B GLU* 3.9 6.3 - - + -
200B GLN 3.4 1.6 - - - +
201B LEU* 3.2 7.7 - - - +
202B TYR* 2.8 76.4 + - + +
204B GLU* 4.6 7.9 - - - +
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Residues in contact with PHE 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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22B PHE* 3.7 31.6 - + - -
23B LEU* 3.9 25.6 - - + -
26B ALA* 4.0 20.2 - - + -
27B VAL* 6.1 0.2 - - + -
30B ILE* 4.2 11.9 - - + -
82B LYS* 3.2 3.2 - - - -
83B VAL* 2.9 47.5 + - + +
85B VAL* 4.2 17.7 - - + -
98B PHE 3.7 11.2 - - - -
99B VAL* 1.3 73.8 - - - +
101B GLU* 1.3 63.5 + - - +
102B ILE* 3.8 7.1 + - + +
130B ILE* 4.6 0.4 - - + -
199B MET* 4.2 17.0 - - + -
200B GLN 3.4 4.7 - - - +
201B LEU* 3.7 38.1 - - + -
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Residues in contact with GLU 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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81B GLU* 3.5 8.5 - - - +
82B LYS* 3.6 21.5 + - + +
99B VAL* 3.9 8.1 - - + -
100B PHE* 1.3 74.7 - - - +
102B ILE* 1.3 59.3 + - - +
103B THR* 5.5 0.7 - - - -
198B LYS 3.8 0.2 - - - +
199B MET* 3.2 8.1 - - - +
200B GLN* 2.8 45.8 + - + +
202B TYR* 2.5 45.4 + - + -
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Residues in contact with ILE 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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19B LEU* 4.1 23.1 - - + -
23B LEU* 5.1 4.7 - - + -
75B LEU* 4.3 10.5 - - + -
80B VAL* 3.6 13.6 - - + +
81B GLU 3.1 16.0 + - - +
83B VAL* 4.2 22.7 - - + -
100B PHE* 3.9 17.3 - - + +
101B GLU* 1.3 79.4 - - - +
103B THR* 1.3 64.6 + - - +
104B GLN* 4.6 11.4 - - + +
153B ARG* 2.7 27.5 + - - +
197B LEU* 3.9 17.7 - - + -
198B LYS 3.6 2.7 - - - -
199B MET* 4.1 20.4 - - + -
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Residues in contact with THR 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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101B GLU 5.5 0.3 - - - -
102B ILE* 1.3 76.9 + - - +
104B GLN* 1.3 66.7 + - - +
105B PRO* 3.6 14.1 - - + +
153B ARG* 3.7 8.9 + - - +
197B LEU* 3.5 6.8 - - - +
198B LYS* 2.8 56.7 + - + +
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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