Contacts of the strand formed by residues 99 - 106 (chain E) in PDB entry 3ZWG
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 THR 99 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48E MET* 3.5 11.0 - - + +
91E ALA* 4.4 4.7 - - + -
92E TYR 3.4 7.4 - - - +
94E MET* 4.8 1.1 - - - -
98E ASN* 1.3 75.0 + - - +
100E LEU* 1.3 74.9 + - - +
101E ALA* 3.8 5.8 + - + +
120E ARG 3.7 0.5 - - - +
121E VAL* 3.4 8.3 - - - +
122E TYR* 2.8 51.8 + - + -
124E GLY 2.8 19.3 + - - -
125E GLN* 3.3 4.5 - - - -
126E LYS* 2.9 36.0 + - + +
132E MET* 4.9 0.7 - - + -
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ILE* 4.8 3.1 - - + -
45E TRP* 3.5 43.3 - - + -
90E ILE 3.6 1.0 - - - +
91E ALA* 3.4 4.3 - - - -
92E TYR* 2.9 42.9 + - + +
94E MET* 4.3 20.9 - - + +
99E THR* 1.3 73.2 - - - +
101E ALA* 1.3 61.1 + - - +
102E VAL* 4.6 16.4 - - + -
119E VAL* 4.0 21.5 - - + -
120E ARG 3.9 1.3 - - - +
121E VAL* 4.0 22.4 - - + +
154E LEU* 4.1 8.1 - - + -
158E LEU* 5.4 0.2 - - + -
176E VAL* 4.1 11.9 - - + -
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E VAL* 4.4 0.2 - - + -
90E ILE 3.2 5.4 - - - +
91E ALA* 5.2 0.2 - - - -
99E THR* 4.6 3.4 - - + -
100E LEU* 1.3 76.1 - - - +
102E VAL* 1.3 68.3 + - - +
103E LEU 4.3 0.2 - - - -
118E ASN 3.9 0.5 - - - +
119E VAL* 3.5 1.9 - - - +
120E ARG* 3.0 37.7 + - + +
122E TYR* 3.9 17.5 - - + -
132E MET* 3.9 28.3 - - - -
136E LEU* 4.0 10.7 - - + +
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E VAL* 5.4 0.4 - - + -
37E ILE* 4.0 26.5 - - + -
88E GLY 3.8 0.5 - - - +
89E VAL* 3.1 6.8 - - - -
90E ILE* 2.7 53.4 + - + +
100E LEU* 4.6 13.5 - - + -
101E ALA* 1.3 81.2 - - - +
103E LEU* 1.3 70.3 + - - +
104E PHE* 4.3 1.8 - - + -
118E ASN 3.3 9.4 - - - +
119E VAL* 4.2 17.9 - - + -
172E LEU* 4.4 6.5 - - + -
174E ILE* 3.6 23.8 - - + -
176E VAL* 6.2 0.2 - - + -
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E GLY 3.3 12.1 - - - +
89E VAL* 4.3 3.6 - - + -
101E ALA 4.3 0.6 - - - -
102E VAL* 1.3 77.3 - - - +
104E PHE* 1.3 88.5 + - - +
105E SER* 4.2 1.3 - - - +
116E TRP* 5.1 1.8 - - + -
117E TRP* 3.1 11.8 - - - +
118E ASN* 2.9 49.3 + - + +
133E TYR* 4.2 26.5 - - + -
136E LEU* 3.5 45.5 - - + +
137E TYR* 3.8 17.0 - - + +
142E PRO* 4.2 8.1 - - + -
172E LEU* 4.4 0.2 - - - +
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Residues in contact with PHE 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ILE* 3.8 40.4 - - + -
35E VAL* 4.9 5.8 - - + -
50E THR* 4.5 2.7 - - + -
52E PHE* 3.9 19.7 - + - -
73E TYR* 5.2 4.3 - + - -
75E GLY* 5.7 0.9 - - - -
86E VAL* 3.9 31.4 - - + -
87E VAL* 3.2 2.2 - - - -
88E GLY* 2.7 73.8 + - - +
89E VAL 4.0 0.2 - - - -
90E ILE* 4.0 30.7 - - + -
102E VAL* 4.3 5.8 - - + -
103E LEU* 1.3 82.5 - - - +
105E SER* 1.3 59.5 + - - +
106E VAL* 5.2 0.2 - - + -
116E TRP 3.5 5.6 - - - +
117E TRP* 4.4 0.2 - - - +
164E MET* 4.8 1.1 - - + -
172E LEU* 4.2 11.2 - - + -
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Residues in contact with SER 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E VAL* 3.2 23.7 - - - +
103E LEU* 4.2 1.3 - - - +
104E PHE* 1.3 75.3 - - - +
106E VAL* 1.3 61.4 + - - +
107E PRO* 3.5 10.5 - - - +
115E ASN* 3.4 8.0 - - - +
116E TRP* 2.7 39.7 + - - +
137E TYR* 3.5 36.3 + - - -
164E MET* 4.1 0.5 - - - +
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Residues in contact with VAL 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ARG* 4.2 7.4 - - - -
32E LYS 4.9 0.2 - - - +
33E ILE* 4.0 11.9 - - + -
85E GLY* 3.0 6.1 - - - -
86E VAL* 2.8 53.8 + - + +
87E VAL* 3.9 3.0 - - - +
105E SER* 1.3 74.7 + - - +
107E PRO* 1.3 60.9 - - - +
110E TYR* 3.6 11.9 - - - +
115E ASN* 3.3 11.7 - - - +
164E MET* 3.8 11.7 - - + -
167E SER 4.2 1.8 - - - +
168E GLY* 3.8 25.1 - - - +
170E ALA* 3.7 23.3 - - + -
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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