Contacts of the strand formed by residues 95 - 99 (chain A) in PDB entry 5WWT
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 VAL 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR* 4.6 6.5 - - - -
55A VAL 3.6 8.1 - - - +
56A ARG* 4.9 4.7 - - + -
64A VAL* 5.7 0.2 - - - -
88A GLN* 3.9 4.7 - - - +
89A HIS* 3.3 26.2 + - + +
92A LEU* 3.2 26.8 + - + +
93A GLN 3.4 1.6 + - - -
94A ASP* 1.3 94.9 - - - +
96A LEU* 1.3 67.5 + - - +
97A LEU* 3.7 24.5 - - + -
219A GLN 5.9 0.4 - - - +
221A LEU* 3.9 14.1 - - + -
224A ALA* 3.9 26.5 - - + -
228A HIS* 5.2 0.4 - - - +
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Residues in contact with LEU 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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53A THR 3.9 0.6 - - - +
54A THR* 3.4 0.3 - - - -
55A VAL* 2.9 45.3 + - + +
57A VAL* 3.7 27.1 - - + -
64A VAL* 3.7 23.1 - - + +
67A VAL* 4.0 2.2 - - + -
68A LYS* 3.9 28.5 - - + +
71A LEU* 3.9 25.4 - - + -
86A ILE* 4.0 16.2 - - + -
87A LEU 3.5 11.7 - - - +
88A GLN* 4.4 9.0 - - + -
94A ASP 4.2 0.2 + - - -
95A VAL* 1.3 76.5 - - - +
97A LEU* 1.3 69.4 + - - +
98A ILE* 5.4 0.2 - - - -
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Residues in contact with LEU 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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52A PHE* 4.0 14.1 - - + -
53A THR 3.8 1.8 - - - -
54A THR* 3.6 24.7 - - + -
85A PRO 3.8 0.7 - - - +
86A ILE* 3.4 4.2 - - - -
87A LEU* 2.9 49.4 + - + +
89A HIS* 3.7 28.5 - - + +
95A VAL* 3.7 19.3 - - + +
96A LEU* 1.3 84.2 - - - +
98A ILE* 1.3 64.2 + - - +
99A PRO* 4.2 2.4 - - - +
221A LEU* 4.0 8.7 - - + -
448A LEU* 4.0 19.1 - - + -
451A ALA* 3.8 20.6 - - + -
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Residues in contact with ILE 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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52A PHE* 3.5 4.2 - - - -
53A THR* 2.8 48.0 + - + +
55A VAL* 4.6 8.5 - - + -
71A LEU* 4.8 5.8 - - + -
75A LEU* 3.7 33.7 - - + -
79A PHE* 5.5 0.7 - - + -
84A VAL* 4.3 7.0 - - + -
85A PRO 3.9 3.1 - - - +
86A ILE* 3.8 25.1 - - + -
96A LEU 5.4 0.2 - - - -
97A LEU* 1.3 79.3 - - - +
99A PRO* 1.3 80.0 - - + +
206A PRO* 4.3 23.6 - - + -
208A PHE* 4.3 18.6 - - + -
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Residues in contact with PRO 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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51A SER 3.7 1.8 - - - +
52A PHE* 3.6 31.6 - - + -
79A PHE* 6.1 0.7 - - - -
84A VAL* 4.7 6.5 - - + +
85A PRO* 3.1 46.4 - - + +
87A LEU* 5.8 0.9 - - + +
97A LEU 4.2 1.3 - - - +
98A ILE* 1.3 96.3 - - + +
100A VAL* 1.3 62.1 + - - +
101A ILE* 3.8 8.9 + - - +
204A LEU 4.7 2.1 - - - +
206A PRO* 5.7 1.4 - - - +
434A THR* 4.7 7.2 - - + +
439A LEU* 3.8 20.6 - - + -
447A MET* 4.7 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