Contacts of the strand formed by residues 94 - 103 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A VAL* 3.9 14.6 - - + -
87A ILE 3.5 7.9 - - - +
88A LEU* 3.7 7.8 - - + -
92A HIS 3.7 1.8 - - - +
93A ARG* 1.3 81.9 - - + +
95A VAL* 1.3 59.7 + - - +
97A LYS* 4.3 7.0 - - + -
177A GLN 3.5 16.6 - - - +
178A ASP 3.3 25.1 - - - +
179A VAL 4.3 1.6 - - - -
180A HIS 3.6 20.6 - - - +
181A MET* 3.1 21.3 - - + +
206A ARG* 2.9 26.4 + - - +
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Residues in contact with VAL 95 (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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87A ILE* 2.8 28.6 + - + +
89A ASP* 4.1 20.6 - - + +
93A ARG* 3.2 11.2 + - - +
94A PRO* 1.3 77.6 - - - +
96A GLU* 1.3 67.9 + - - +
140A ASN* 3.7 20.2 - - - +
141A PRO* 4.5 4.3 - - + -
144A CYS* 4.2 9.4 - - - -
181A MET* 3.7 5.4 - - - -
205A GLU* 3.6 0.2 - - - -
206A ARG* 2.9 36.0 + - - +
209A LYS* 3.7 29.1 - - + -
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Residues in contact with GLU 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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34A ARG* 2.7 52.3 + - - +
85A VAL 3.9 0.2 - - - +
86A VAL* 4.0 0.5 - - - +
87A ILE* 2.8 36.8 + - + +
95A VAL* 1.3 87.7 - - - +
97A LYS* 1.3 67.4 + - - +
98A PHE* 3.8 12.5 - - + -
137A LEU* 3.7 15.9 - - - +
140A ASN* 3.1 24.9 + - - +
181A MET* 4.3 0.2 - - - -
203A VAL* 4.6 2.2 - - + -
204A GLU 3.3 7.4 - - - +
205A GLU* 4.3 7.0 - - + -
209A LYS* 2.8 16.0 + - - +
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Residues in contact with LYS 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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84A VAL* 3.9 18.6 - - + -
85A VAL 3.5 3.8 - - - -
86A VAL* 4.1 15.9 - - + -
94A PRO* 4.3 13.5 - - - -
96A GLU* 1.3 80.9 - - - +
98A PHE* 1.3 64.0 + - - +
99A VAL* 3.7 8.8 + - + +
149A LEU* 5.6 2.1 - - + +
178A ASP 4.8 2.0 - - - -
179A VAL* 2.6 47.1 + - - +
181A MET* 4.2 19.8 - - - +
202A TYR 3.7 0.9 - - - +
203A VAL* 3.1 6.2 - - - -
204A GLU* 2.8 54.6 + - + +
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Residues in contact with PHE 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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30A ILE* 3.7 50.7 - - + -
33A VAL* 5.4 0.2 - - + -
34A ARG* 3.9 23.8 - - + -
84A VAL* 3.3 4.3 - - - -
85A VAL* 2.8 44.6 + - + +
87A ILE* 4.0 8.5 - - + -
96A GLU* 3.8 23.1 - - + -
97A LYS* 1.3 72.6 - - - +
99A VAL* 1.3 61.5 + - - +
100A PHE* 3.7 10.3 - - + -
130A ILE* 5.2 3.4 - - + -
133A CYS* 4.0 17.5 - - - -
137A LEU* 4.1 5.4 - - + -
189A LEU* 4.4 9.4 - - + -
201A LEU* 4.2 5.6 - - + -
202A TYR 3.7 3.1 - - - -
203A VAL* 3.2 29.6 - - + -
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Residues in contact with VAL 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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82A LYS* 3.9 16.8 - - + +
83A VAL 3.9 2.2 - - - -
84A VAL* 4.0 20.0 - - + -
97A LYS* 3.9 19.1 - - + +
98A PHE* 1.3 74.1 - - - +
100A PHE* 1.3 62.0 + - - +
101A GLU* 3.9 15.5 - - + -
200A GLN 3.4 2.6 - - - +
201A LEU* 3.2 5.9 - - - +
202A TYR* 2.8 74.8 + - + +
204A GLU* 4.7 6.7 - - + +
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Residues in contact with PHE 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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22A PHE* 3.7 31.4 - + - -
23A LEU* 3.9 23.3 - - + -
26A ALA* 3.9 19.7 - - + -
27A VAL* 6.1 0.2 - - + -
30A ILE* 4.0 20.6 - - + -
82A LYS* 3.2 3.1 - - - -
83A VAL* 2.9 46.9 + - + +
85A VAL* 4.3 9.6 - - + -
98A PHE 3.7 13.7 - - - -
99A VAL* 1.3 71.3 - - - +
101A GLU* 1.3 64.0 + - - +
102A ILE* 3.7 16.7 + - + +
130A ILE* 4.5 0.4 - - + -
199A MET* 4.2 11.4 - - + -
200A GLN 3.4 5.4 - - - -
201A LEU* 3.8 36.3 - - + -
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Residues in contact with GLU 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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81A GLU* 3.5 7.2 - - + +
82A LYS* 3.4 31.2 + - + +
99A VAL* 3.9 9.2 - - + -
100A PHE* 1.3 73.2 - - - +
102A ILE* 1.3 58.8 + - - +
198A LYS 4.0 0.2 - - - +
199A MET* 3.2 8.0 - - - +
200A GLN* 2.8 50.6 + - + +
202A TYR* 2.7 33.2 + - + -
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Residues in contact with ILE 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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19A LEU* 4.1 30.1 - - + -
23A LEU* 5.0 5.4 - - + -
75A LEU* 4.5 13.7 - - + -
80A VAL* 3.5 13.1 - - + +
81A GLU 2.9 14.0 + - - +
83A VAL* 4.1 24.7 - - + +
100A PHE* 3.8 18.6 - - + +
101A GLU* 1.3 80.8 - - - +
103A THR* 1.3 62.6 + - - +
104A GLN* 4.5 10.1 - - + +
153A ARG* 2.8 30.0 + - - -
197A LEU* 4.1 8.3 - - + -
198A LYS 3.7 2.5 - - - -
199A MET* 4.0 19.5 - - - -
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Residues in contact with THR 103 (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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102A ILE* 1.3 77.8 + - - +
104A GLN* 1.3 74.2 + - - +
105A PRO* 3.3 3.7 - - + +
153A ARG* 3.6 15.0 + - - +
197A LEU* 3.5 3.8 - - - +
198A LYS* 2.7 70.7 + - - +
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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