Contacts of the strand formed by residues 130 - 139 (chain E) in PDB entry 4QAE
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 ARG 130 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E LEU* 4.6 26.5 - - + -
40E GLU* 2.6 42.4 + - - +
126E VAL* 3.5 5.7 - - - +
127E TRP* 2.9 62.3 + - - +
128E GLN* 3.2 15.2 + - - +
129E ASN* 1.3 80.9 - - - +
131E GLU* 1.3 65.9 + - - +
132E VAL* 4.2 4.0 - - + +
13T CYS 3.2 20.0 + - - -
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Residues in contact with GLU 131 (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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7E LEU* 6.1 0.7 - - - +
8E ILE 4.7 0.7 - - - +
10E ALA* 3.5 34.7 + - + +
39E ASN* 3.0 18.9 + - - -
40E GLU* 4.8 0.7 - - - +
124E LYS* 3.1 34.6 + - + -
125E VAL 3.4 7.6 - - - +
126E VAL* 4.7 14.6 - - + +
130E ARG* 1.3 79.1 - - - +
132E VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 132 (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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39E ASN* 3.5 11.0 - - - +
40E GLU* 3.5 37.0 - - + +
124E LYS* 3.3 2.9 - - - +
125E VAL* 2.8 38.3 + - + +
127E TRP* 4.1 12.8 - - + -
130E ARG* 4.2 7.2 - - + +
131E GLU* 1.3 76.3 - - - +
133E PHE* 1.3 63.5 + - - +
134E TRP* 4.0 2.8 - - + -
10T CYS* 3.8 10.8 - - - -
11T CYS 3.7 23.3 - - - +
13T CYS* 3.7 21.5 - - - -
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Residues in contact with PHE 133 (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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8E ILE* 4.5 0.9 - - + -
9E PRO 3.6 19.1 - - - -
10E ALA* 3.5 18.4 - - + -
11E PRO* 3.8 13.7 - - + -
38E GLY* 3.2 19.4 - - - -
39E ASN* 2.9 42.2 + - + +
40E GLU 4.8 0.3 + - - -
122E PHE* 3.7 26.2 - + + -
123E PHE 3.1 13.9 - - - +
124E LYS* 4.2 6.7 - - + -
132E VAL* 1.3 77.2 - - - +
134E TRP* 1.3 73.0 + - - +
135E VAL* 5.0 0.4 - - + -
159E LEU* 4.0 23.3 - - + -
161E LEU* 3.6 41.3 - - + -
11T CYS 5.0 0.7 - - - +
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Residues in contact with TRP 134 (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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36E LEU* 3.6 25.8 - - + -
37E ALA 3.1 13.7 - - - +
38E GLY* 3.9 4.5 - - - -
41E VAL* 5.1 0.2 - - + -
52E TRP* 4.9 1.6 - - - -
81E GLN* 6.2 0.4 - - - -
122E PHE* 3.6 2.3 - - - -
123E PHE* 2.8 78.8 + + + +
125E VAL* 4.0 16.8 - - + -
132E VAL 4.0 13.2 - - - -
133E PHE* 1.3 86.8 - - - +
135E VAL* 1.3 63.6 + - - +
136E THR* 4.2 6.0 - - + +
9T PHE* 3.6 37.5 - + - -
10T CYS* 3.6 23.3 - - - -
11T CYS* 3.7 39.9 - - + +
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Residues in contact with VAL 135 (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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36E LEU* 3.4 5.6 - - - +
37E ALA* 2.8 36.0 + - + +
111E VAL* 5.6 0.2 - - + -
120E MET* 4.5 3.1 - - + -
121E VAL 3.2 15.5 - - - +
122E PHE* 4.1 12.3 - - + -
133E PHE* 4.8 4.7 - - + -
134E TRP* 1.3 78.8 - - - +
136E THR* 1.3 69.8 + - - +
152E PHE* 3.7 23.4 - - + -
155E PHE* 4.1 22.9 - - + -
156E SER* 4.8 5.8 - - - +
159E LEU* 3.9 28.3 - - + -
161E LEU* 5.4 2.5 - - + -
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Residues in contact with THR 136 (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 VAL* 4.3 10.1 - - + -
35E GLY 3.4 5.2 - - - -
36E LEU* 4.0 17.7 - - + -
52E TRP* 4.3 10.1 - - + -
119E ALA 3.7 0.5 - - - +
120E MET* 3.1 8.5 - - - +
121E VAL* 2.9 30.1 + - - +
123E PHE* 3.4 26.6 - - + -
134E TRP* 4.2 4.9 - - + -
135E VAL* 1.3 77.8 - - - +
137E LEU* 1.3 59.6 + - - +
138E TYR* 3.3 33.6 - - + +
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Residues in contact with LEU 137 (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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32E TYR 3.6 0.2 - - - +
33E VAL* 3.7 1.7 - - - -
34E VAL* 2.8 40.1 + - + -
35E GLY* 2.8 20.0 + - - +
118E HIS* 4.8 7.9 - - + -
119E ALA 3.4 15.7 - - - +
120E MET* 3.9 14.4 - - + -
136E THR* 1.3 70.9 - - - +
138E TYR* 1.3 55.4 + - - +
144E LEU* 3.7 28.7 - - + -
148E LEU* 4.2 9.6 - - + +
149E LYS* 4.0 28.0 - - + +
152E PHE* 3.7 38.3 - - + -
168E PHE* 4.5 1.1 - - + -
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Residues in contact with TYR 138 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E PHE* 4.1 2.0 - + - -
31E TRP* 3.4 35.9 - + + -
32E TYR 3.1 9.2 - - - -
33E VAL* 4.0 14.8 - - + -
52E TRP* 5.9 0.2 - - - -
54E THR* 3.7 18.1 + - - +
56E TYR* 2.7 45.8 + + - -
118E HIS* 3.2 6.1 - - - -
119E ALA* 2.8 40.2 + - + +
121E VAL* 3.6 23.1 - - + -
123E PHE* 3.6 12.5 - - - -
136E THR* 3.3 33.5 - - + +
137E LEU* 1.3 74.5 - - - +
139E GLY* 1.3 57.4 + - - +
144E LEU* 3.5 9.0 - - - +
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Residues in contact with GLY 139 (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 TRP* 3.6 7.5 - - - -
32E TYR 2.8 34.1 + - - -
34E VAL* 3.8 3.5 - - - +
117E GLN 3.3 7.9 - - - -
138E TYR* 1.3 74.8 - - - +
140E ARG* 1.3 64.7 + - - -
141E THR 3.2 15.8 - - - +
144E LEU* 4.0 12.3 - - - -
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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