Contacts of the strand formed by residues 94 - 103 (chain A) in PDB entry 3WHD
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 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A CYS* 3.8 2.1 - - - -
90A ALA* 3.7 3.5 - - - +
91A PHE 3.0 30.4 + - - +
92A GLN 3.0 15.8 + - - -
93A SER* 1.3 85.3 - - - +
95A CYS* 1.3 65.2 + - - +
96A TYR* 3.6 27.2 + - + +
127A GLU* 4.5 1.8 + - - -
208A LYS* 3.7 27.7 - - + +
209A ILE 3.8 2.9 - - - +
210A PRO* 3.4 21.1 - - - +
211A GLY 3.9 0.7 - - - +
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Residues in contact with CYS 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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84A CYS* 2.0 57.2 - - + -
85A PRO* 4.1 4.0 - - + -
88A TRP* 3.7 11.9 - - + -
89A ARG 3.3 5.6 - - - +
94A ASN* 1.3 74.5 - - - +
96A TYR* 1.3 64.1 + - - +
208A LYS* 3.2 4.9 - - - +
209A ILE* 2.9 52.1 + - + +
210A PRO 4.5 0.4 - - - -
211A GLY* 3.6 20.9 - - - -
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Residues in contact with TYR 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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88A TRP* 3.5 6.2 - - - -
89A ARG* 2.9 46.3 + - + +
91A PHE* 4.0 19.5 + - + -
94A ASN* 3.6 35.4 + - + +
95A CYS* 1.3 73.6 - - - +
97A PHE* 1.3 62.5 + - - +
98A PRO* 4.3 1.6 - - - -
120A MET* 3.5 31.4 - - + -
127A GLU* 2.6 33.7 + - + +
130A PHE* 3.9 14.6 - + - -
131A ILE* 3.7 21.3 - - + -
206A ILE* 4.5 1.1 - - + -
207A CYS 3.2 6.7 - - - +
208A LYS* 3.5 33.0 - - + -
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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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87A ASP* 3.3 46.0 - - + -
88A TRP* 3.6 46.9 - + + -
89A ARG* 6.2 1.6 - - + -
96A TYR* 1.3 73.2 - - - +
98A PRO* 1.3 83.6 - - + +
99A LEU* 3.6 26.9 + - + +
115A MET* 5.8 1.3 - - + -
206A ILE* 4.4 1.3 - - - -
207A CYS* 2.8 33.6 + - + +
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Residues in contact with PRO 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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89A ARG* 4.7 15.0 - - + +
96A TYR 4.3 4.0 - - - +
97A PHE* 1.3 105.2 - - + +
99A LEU* 1.3 61.6 + - - +
100A THR* 5.3 2.7 - - + +
131A ILE* 4.3 11.2 - - + -
134A PHE* 4.2 23.8 - - + +
135A LEU* 3.9 29.2 - - + -
141A TYR* 4.0 8.5 - - + +
205A ARG 3.4 7.4 - - - +
206A ILE* 4.2 4.7 - - + -
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Residues in contact with LEU 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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97A PHE* 3.9 26.2 - - + +
98A PRO* 1.3 82.4 - - - +
100A THR* 1.3 62.1 + - - +
101A ASP* 3.7 4.0 - - - +
111A ASN* 3.5 24.5 - - - +
115A MET* 3.8 20.9 - - + -
141A TYR* 4.3 1.0 - - - -
204A SER* 3.0 5.7 - - - -
205A ARG* 2.7 61.0 + - + +
207A CYS* 4.0 8.5 - - - -
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Residues in contact with THR 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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98A PRO* 5.3 2.2 - - + -
99A LEU* 1.3 78.3 - - - +
101A ASP* 1.3 65.4 + - - +
102A ASN* 3.5 6.1 + - - +
136A ASP* 5.5 1.6 - - + -
139A LEU* 3.8 27.8 - - + +
141A TYR* 3.9 15.3 - - + +
204A SER* 3.3 15.7 + - - +
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Residues in contact with ASP 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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99A LEU* 4.2 2.6 - - - +
100A THR* 1.3 77.7 + - - +
102A ASN* 1.3 64.8 + - - +
103A LYS* 3.3 23.3 + - - +
203A ALA 3.8 3.2 - - - +
204A SER* 4.5 0.3 - - - -
205A ARG* 3.0 49.1 + - - -
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Residues in contact with ASN 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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100A THR 3.5 6.9 + - - +
101A ASP* 1.3 73.0 - - - +
103A LYS* 1.3 66.0 + - - +
107A GLU* 5.1 0.3 - - - +
139A LEU* 5.9 2.6 - - - +
202A GLU* 4.1 29.4 + - + +
203A ALA* 3.3 28.5 - - - -
204A SER* 3.6 3.5 + - - -
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Residues in contact with LYS 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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101A ASP* 3.3 26.2 + - - +
102A ASN* 1.3 80.9 - - - +
104A THR* 1.3 66.1 + - - +
107A GLU* 3.7 37.2 + - + +
108A SER* 3.5 13.3 + - - +
110A ARG* 6.0 1.8 - - - +
111A ASN* 4.2 11.9 - - + +
142A PHE* 3.4 4.2 - - - -
202A GLU* 3.3 9.8 - - - -
203A ALA 3.0 28.3 + - - +
205A ARG* 3.5 27.6 - - - +
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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