Contacts of the strand formed by residues 203 - 210 (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 ALA 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ASP 3.8 1.6 - - - +
102A ASN* 3.3 15.2 + - - -
103A LYS* 3.0 30.1 + - - +
108A SER* 4.4 2.3 + - - -
140A SER* 3.5 26.7 - - - +
142A PHE* 3.9 15.2 - - + -
184A VAL* 4.4 6.7 - - + -
201A PHE* 6.0 0.7 - - + -
202A GLU* 1.3 76.5 - - - +
204A SER* 1.3 70.5 + - - +
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Residues in contact with SER 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU 3.0 16.6 - - - -
100A THR* 3.3 20.9 + - - -
101A ASP 4.5 6.1 - - - -
102A ASN* 3.6 3.2 + - - -
139A LEU* 3.7 17.5 - - - +
140A SER 3.0 14.1 + - - -
141A TYR* 3.7 16.2 - - - -
142A PHE* 2.8 26.7 + - - +
203A ALA* 1.3 80.2 - - - +
205A ARG* 1.3 66.1 + - - +
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Residues in contact with ARG 205 (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* 3.4 2.8 - - - +
99A LEU* 2.7 58.3 + - + +
101A ASP* 3.0 46.5 + - - -
103A LYS* 3.5 20.2 - - - +
108A SER* 3.6 34.3 + - - +
111A ASN* 2.7 41.8 + - - +
112A CYS* 4.4 4.7 - - - -
119A LEU* 3.8 14.8 - - + -
141A TYR* 3.6 3.8 - - - +
142A PHE* 3.8 8.5 - - + +
203A ALA 5.0 0.2 + - - -
204A SER* 1.3 80.1 - - - +
206A ILE* 1.3 65.0 + - - +
207A CYS* 4.5 4.7 - - - -
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Residues in contact with ILE 206 (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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96A TYR* 4.5 2.2 - - + -
97A PHE 3.7 9.2 - - - +
98A PRO* 4.3 2.9 - - + -
112A CYS* 4.4 1.1 - - - -
119A LEU* 3.5 6.2 - - - +
120A MET* 2.8 56.5 + - + -
131A ILE* 4.0 26.5 - - + -
135A LEU* 3.9 19.3 - - + -
141A TYR* 3.9 26.2 - - + -
142A PHE 3.3 7.6 + - - +
143A LEU* 4.1 11.4 - - + -
185A LEU* 4.1 19.1 - - + -
205A ARG* 1.3 79.2 - - - +
207A CYS* 1.3 65.9 + - - +
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Residues in contact with CYS 207 (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* 3.8 13.9 - - + -
96A TYR* 3.2 4.9 - - - -
97A PHE* 2.8 36.1 + - + +
99A LEU* 4.0 13.5 - - - -
111A ASN* 4.3 1.3 - - - -
112A CYS* 2.0 52.5 - - + -
115A MET* 3.5 15.3 - - + -
117A ALA* 4.1 9.4 - - + -
118A HIS 3.5 4.0 - - - -
205A ARG* 4.5 3.6 - - - -
206A ILE* 1.3 76.6 - - - +
208A LYS* 1.3 59.7 + - - +
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Residues in contact with LYS 208 (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* 4.5 0.2 - - - -
94A ASN* 3.7 31.0 - - + +
95A CYS 3.2 7.0 - - - +
96A TYR* 3.5 27.1 - - + -
117A ALA* 3.4 2.5 - - - +
118A HIS* 2.8 33.9 + - + +
119A LEU 5.0 0.2 - - - +
120A MET* 3.9 12.3 - - - -
121A THR* 3.1 36.6 + - - +
123A SER* 5.7 1.0 + - - -
127A GLU* 2.5 28.5 + - - -
158A ASP* 4.9 7.8 + - - +
207A CYS* 1.3 75.3 - - - +
209A ILE* 1.3 64.9 + - - +
210A PRO* 4.7 2.9 - - + +
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Residues in contact with ILE 209 (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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85A PRO* 4.6 12.1 - - + -
88A TRP* 3.8 21.5 - - + -
94A ASN* 3.8 3.3 - - - +
95A CYS* 2.9 48.2 + - + -
115A MET 3.8 16.8 - - - +
116A GLY* 3.5 22.4 - - - +
117A ALA* 4.1 7.9 - - + +
208A LYS* 1.3 76.5 - - - +
210A PRO* 1.3 88.7 - - + +
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Residues in contact with PRO 210 (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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93A SER 4.8 0.7 - - - +
94A ASN* 3.4 16.8 - - - +
95A CYS* 4.5 0.5 - - - -
116A GLY 5.1 2.9 - - - +
118A HIS* 6.3 3.8 - - + -
208A LYS* 4.7 3.4 - - + +
209A ILE* 1.3 104.0 - - + +
211A GLY* 1.3 69.9 + - - +
212A THR* 4.8 3.6 - - - +
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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