Contacts of the strand formed by residues 124 - 129 (chain A) in PDB entry 3WAP
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.8 9.0 - - + -
47A PRO 3.3 18.3 + - - +
48A VAL* 3.5 10.1 - - + +
49A VAL 3.0 22.9 + - - +
98A VAL* 4.7 10.8 - - + -
110A MET* 6.4 0.7 - - - -
113A ILE* 5.0 14.8 - - + +
114A TYR* 3.7 27.8 - - + -
117A TYR 4.3 17.0 - - - +
118A LYS* 4.5 2.5 - - - +
119A ASP 4.4 0.2 - - - +
122A GLY 3.2 3.2 + - - -
123A PHE* 1.3 71.8 - - - +
125A TYR* 1.3 66.5 + - - +
126A MET* 4.2 21.8 - - + -
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Residues in contact with TYR 125 (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* 3.3 37.3 + + - -
23A LYS* 3.5 49.3 + - + -
31A ARG* 3.5 18.5 + - - -
49A VAL* 3.5 15.9 - - + -
51A GLU* 3.8 16.8 - - + -
98A VAL* 3.8 7.6 - - - +
99A ASN* 3.0 38.9 + - - +
117A TYR 5.1 0.6 + - - -
119A ASP* 4.3 6.3 - - + +
121A ASP* 3.7 11.5 + - - -
123A PHE* 3.4 33.4 + - + -
124A VAL* 1.3 72.8 - - - +
126A MET* 1.3 65.7 + - - +
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Residues in contact with MET 126 (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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48A VAL* 4.0 25.8 - - + -
49A VAL 2.7 14.6 + - - +
50A VAL* 4.4 5.6 - - + -
51A GLU* 2.7 31.2 + - - +
75A MET* 4.1 19.7 - - - +
78A PHE* 3.9 17.5 - - + -
96A LEU* 3.8 33.0 - - + -
97A LEU 3.4 10.3 - - - +
98A VAL* 4.5 12.1 - - + -
99A ASN 4.1 0.7 - - - +
110A MET* 4.3 9.0 - - + -
113A ILE* 5.2 3.4 - - + -
124A VAL* 4.2 13.9 - - + +
125A TYR* 1.3 81.0 - - - +
127A THR* 1.3 68.5 + - - +
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Residues in contact with THR 127 (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 GLU* 2.9 10.1 - - + +
52A ARG 3.6 2.7 - - - +
53A TYR* 3.1 44.6 - - + +
54A PRO* 4.1 4.0 - - + -
96A LEU* 2.9 17.4 - - - +
97A LEU* 2.8 19.3 + - - -
99A ASN 3.8 1.2 - - - -
100A ASN* 2.7 47.9 + - + +
126A MET* 1.3 77.7 + - - +
128A TYR* 1.3 61.8 + - - +
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Residues in contact with TYR 128 (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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50A VAL* 3.7 13.5 - - + -
51A GLU 3.1 8.7 + - - -
52A ARG* 3.0 42.1 - - + +
53A TYR* 2.9 22.0 + - - +
59A LEU* 4.3 10.0 - - + +
60A PRO 3.3 2.6 + - - -
61A PRO* 3.1 31.4 - - - +
62A LEU* 3.6 26.4 + - + +
82A ILE* 5.5 1.1 - - + -
86A MET* 3.2 30.3 - - + -
94A PHE* 3.6 14.8 - + + -
95A TYR 3.6 10.8 - - - +
96A LEU* 3.3 18.6 - - + +
97A LEU* 4.6 0.9 - - - +
127A THR* 1.3 76.9 - - - +
129A ALA* 1.3 57.9 + - - +
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Residues in contact with ALA 129 (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 TYR* 3.6 26.5 - - + -
56A GLU* 3.8 5.6 - - - +
59A LEU* 3.6 7.9 - - - -
94A PHE* 3.6 1.4 - - - +
95A TYR* 3.1 34.0 + - + +
97A LEU* 4.9 8.3 - - + +
100A ASN* 5.2 0.2 - - - +
128A TYR* 1.3 74.6 - - - +
130A SER* 1.3 62.2 + - - +
131A GLN 3.3 17.4 + - - +
132A GLU* 4.3 12.8 - - + +
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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