Contacts of the strand formed by residues 109 - 114 (chain A) in PDB entry 4ZDV
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 LEU 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ILE* 4.4 3.8 - - + -
32A PRO 3.0 14.3 + - - +
33A VAL* 3.3 9.8 - - + +
34A ILE 2.9 22.8 + - - -
83A VAL* 4.1 11.9 - - + -
95A ILE* 4.0 23.3 - - + -
98A ILE* 4.1 15.7 - - + +
99A TYR* 4.0 19.0 - - + -
102A GLU* 3.8 40.2 - - + +
103A LYS* 4.1 2.5 - - - +
107A GLY 4.0 0.6 + - - -
108A PHE* 1.3 71.9 - - - +
110A TYR* 1.3 61.0 + - - +
111A MET* 3.5 31.0 - - + -
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Residues in contact with TYR 110 (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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7A PHE* 3.7 9.5 - + + -
8A LYS* 3.5 39.0 - - + +
16A ARG* 3.5 9.7 - - - -
34A ILE* 3.6 31.6 - - + -
36A GLU* 4.5 8.7 - - - -
82A LEU 4.2 3.1 - - - +
83A VAL* 4.2 14.7 - - - +
84A ASN 4.8 2.8 + - - -
102A GLU 5.4 1.4 + - - -
104A ASP* 3.5 23.3 - - + +
106A ASP* 2.6 31.7 + - - -
108A PHE* 3.4 24.2 + - + -
109A LEU* 1.3 75.2 - - - +
111A MET* 1.3 65.0 + - - +
112A VAL* 5.7 1.8 - - + -
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Residues in contact with MET 111 (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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33A VAL* 3.6 22.2 - - + -
34A ILE 2.8 12.2 + - - +
35A ILE* 4.3 6.5 - - + -
36A GLU* 3.2 25.0 + - - +
60A MET* 3.5 30.7 - - + -
63A LEU* 3.6 24.0 - - + -
81A LEU* 3.8 29.6 - - + -
82A LEU 3.3 9.2 - - - +
83A VAL* 3.7 11.9 - - + -
88A MET* 5.8 0.2 - - - -
95A ILE* 4.1 1.8 - - + -
109A LEU* 3.5 24.5 - - + +
110A TYR* 1.3 79.6 - - - +
112A VAL* 1.3 68.2 + - - +
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Residues in contact with VAL 112 (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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36A GLU* 3.2 17.7 - - + +
37A ARG 5.2 0.4 - - - +
38A TYR* 3.4 44.2 - - + -
81A LEU* 3.6 4.6 - - - -
82A LEU* 2.7 49.1 + - + +
110A TYR* 5.7 2.5 - - + -
111A MET* 1.3 80.1 - - - +
113A TYR* 1.3 63.6 + - - +
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Residues in contact with TYR 113 (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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35A ILE* 4.0 13.9 - - + -
36A GLU 3.0 23.7 + - - -
37A ARG* 3.5 34.4 + - + +
38A TYR* 2.8 25.7 + - - +
44A LEU* 4.0 15.0 - - + -
45A PRO 2.6 29.8 + - - -
46A VAL* 3.5 2.6 - - - -
47A LEU* 2.9 40.4 + - + +
67A ILE* 4.9 1.1 - - + -
71A LEU* 3.7 15.6 - - + +
79A PHE* 3.5 30.1 - + + -
80A PHE 3.1 12.3 - - - +
81A LEU* 4.0 4.9 - - + -
82A LEU* 5.7 0.2 - - - -
112A VAL* 1.3 74.8 - - - +
114A ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 114 (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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38A TYR* 3.8 24.5 - - + -
41A GLU* 3.6 12.6 - - - +
44A LEU* 3.5 13.6 - - - +
79A PHE* 3.8 0.2 - - - -
80A PHE* 2.9 31.2 + - - +
82A LEU* 5.0 7.2 - - + +
113A TYR* 1.3 77.3 - - - +
115A SER* 1.3 62.2 + - - +
116A GLN* 3.3 21.6 + - - +
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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