Contacts of the strand formed by residues 130 - 139 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B LEU* 4.3 27.6 - - + -
40B GLU* 2.7 41.7 + - - +
126B VAL* 3.4 5.7 - - - -
127B TRP* 2.9 63.5 + - - +
128B GLN* 3.2 15.5 + - - +
129B ASN* 1.3 74.9 - - - +
131B GLU* 1.3 64.2 + - - +
132B VAL* 4.0 6.8 + - + +
13Q CYS 3.3 18.8 + - - -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 6.0 2.3 - - - +
8B ILE 4.7 0.3 - - - +
9B PRO* 5.6 0.2 - - - +
10B ALA* 3.6 31.0 + - + +
39B ASN* 3.0 19.4 + - - -
40B GLU* 4.9 0.9 - - - +
124B LYS* 3.0 34.6 + - + -
125B VAL 3.4 3.6 - - - +
126B VAL* 4.3 19.9 - - + +
130B ARG* 1.3 79.4 - - - +
132B VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN* 3.5 10.5 - - - +
40B GLU* 3.5 37.2 - - + +
124B LYS* 3.3 3.6 - - - +
125B VAL* 2.9 35.7 + - + +
127B TRP* 4.2 10.8 - - + -
130B ARG* 4.1 10.5 - - + +
131B GLU* 1.3 75.9 - - - +
133B PHE* 1.3 63.9 + - - +
134B TRP* 4.1 3.5 - - + -
10Q CYS* 3.8 11.2 - - - -
11Q CYS 3.6 24.0 - - - +
13Q CYS* 3.8 21.1 - - - +
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ILE* 4.5 1.6 - - + -
9B PRO 3.6 12.6 - - - -
10B ALA* 3.5 16.4 - - + -
11B PRO* 3.6 22.4 - - + -
38B GLY* 3.1 2.8 - - - -
39B ASN* 2.9 63.9 + - + +
40B GLU 4.7 0.2 + - - -
122B PHE* 3.6 26.9 - + + -
123B PHE 3.1 12.8 - - - +
124B LYS* 4.3 6.7 - - + -
132B VAL* 1.3 77.0 - - - +
134B TRP* 1.3 71.4 + - - +
135B VAL* 4.9 1.8 - - + -
159B LEU* 4.0 23.3 - - + -
161B LEU* 3.6 39.3 - - + -
11Q CYS 5.0 0.7 - - - +
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Residues in contact with TRP 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 3.7 26.2 - - + -
37B ALA 3.0 13.9 - - - +
38B GLY* 3.9 4.7 - - - -
41B VAL* 5.1 0.2 - - + -
52B TRP* 4.9 1.6 - - - -
81B GLN* 6.2 0.7 - - - -
122B PHE* 3.6 2.3 - - - -
123B PHE* 2.8 80.8 + + + +
125B VAL* 3.9 16.4 - - + -
132B VAL 4.1 11.9 - - - -
133B PHE* 1.3 84.6 - - - +
135B VAL* 1.3 64.3 + - - +
136B THR* 4.2 6.4 - - + +
9Q PHE* 3.5 38.1 - + - -
10Q CYS* 3.6 17.5 - - - -
11Q CYS* 3.7 45.6 - - + +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 3.4 6.3 - - - +
37B ALA* 2.6 37.8 + - + +
120B MET* 4.5 3.1 - - + -
121B VAL 3.2 14.8 - - - +
122B PHE* 4.0 13.9 - - + -
133B PHE* 4.9 3.8 - - + -
134B TRP* 1.3 79.4 - - - +
136B THR* 1.3 69.5 + - - +
152B PHE* 3.7 25.4 - - + -
155B PHE* 4.1 22.7 - - + -
156B SER* 4.8 5.8 - - - +
159B LEU* 3.8 28.3 - - + -
161B LEU* 5.6 1.6 - - + -
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 4.2 10.8 - - + -
35B GLY 3.4 5.4 - - - -
36B LEU* 4.1 17.7 - - + -
52B TRP* 4.4 10.5 - - + -
119B ALA 3.7 0.5 - - - +
120B MET* 3.2 8.3 - - - +
121B VAL* 2.9 30.7 + - - +
123B PHE* 3.4 25.6 - - + -
134B TRP* 4.2 4.9 - - + -
135B VAL* 1.3 76.1 - - - +
137B LEU* 1.3 59.3 + - - +
138B TYR* 3.3 34.0 + - + -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 3.6 1.7 - - - -
34B VAL* 2.8 40.9 + - + -
35B GLY* 2.8 19.5 + - - +
118B HIS* 4.9 6.7 - - + -
119B ALA 3.4 14.4 - - - +
120B MET* 4.0 14.1 - - + -
136B THR* 1.3 71.0 - - - +
138B TYR* 1.3 55.8 + - - +
144B LEU* 3.6 31.2 - - + -
148B LEU* 4.3 9.9 - - + +
149B LYS* 4.0 26.5 - - + +
152B PHE* 3.8 39.4 - - + -
168B PHE* 4.5 1.1 - - + -
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Residues in contact with TYR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 4.1 2.2 - + - -
31B TRP* 3.5 37.2 - + + -
32B TYR 3.2 11.2 - - - +
33B VAL* 4.0 15.7 - - + -
52B TRP* 5.8 0.4 - + - -
54B THR* 3.8 17.6 + - - +
56B TYR* 2.6 46.3 + + - -
118B HIS* 3.2 6.2 - - - -
119B ALA* 2.7 39.6 + - + +
121B VAL* 3.6 22.0 - - + -
123B PHE* 3.5 12.3 - - - -
136B THR* 3.3 34.1 - - + -
137B LEU* 1.3 73.7 - - - +
139B GLY* 1.3 59.6 + - - +
144B LEU* 3.6 9.5 - - - +
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B TRP* 3.6 6.4 - - - -
32B TYR 2.7 34.0 + - - -
34B VAL* 3.9 8.3 - - - +
117B GLN 3.3 9.4 - - - -
138B TYR* 1.3 73.4 - - - +
140B ARG* 1.3 63.4 + - - -
141B THR 3.2 16.0 + - - +
144B LEU* 4.1 7.6 - - - -
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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