Contacts of the strand formed by residues 7 - 16 (chain V) in PDB entry 3MQT
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 ILE 7 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6V ASN* 1.3 72.6 - - - +
8V VAL* 1.3 63.6 + - - +
9V SER 3.9 11.9 - - - +
10V VAL* 4.4 2.9 - - + -
31V VAL* 3.6 26.0 - - + -
32V THR 3.7 4.3 - - - +
33V ASP* 4.1 1.1 - - - +
70V VAL* 3.5 33.7 - - + +
71V ILE* 3.6 12.1 - - + +
72V GLY* 2.7 29.1 + - - -
73V ARG* 3.0 19.4 + - + +
74V ASP 4.9 0.2 - - - -
75V PRO* 4.0 17.7 - - + -
81V ASN* 5.1 1.1 - - - +
109V LEU* 3.4 32.3 - - + -
112V LEU* 4.0 6.5 - - + -
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Residues in contact with VAL 8 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7V ILE* 1.3 74.7 - - - +
9V SER* 1.3 73.2 + - - +
32V THR* 2.8 14.9 + - + +
33V ASP 4.1 11.0 - - - +
34V GLU* 3.9 33.2 - - - +
71V ILE* 3.7 19.4 - - - +
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Residues in contact with SER 9 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7V ILE* 3.8 0.8 - - - +
8V VAL* 1.3 88.9 - - - +
10V VAL* 1.3 69.6 + - - +
11V GLU* 5.9 1.1 - - - +
30V LYS 3.9 1.1 + - - +
31V VAL* 3.4 5.9 - - - +
32V THR* 3.0 47.3 + - - +
71V ILE* 3.7 5.6 - - - +
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Residues in contact with VAL 10 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7V ILE* 4.4 0.4 - - + -
9V SER* 1.3 81.5 - - - +
11V GLU* 1.3 67.4 + - - +
12V PHE* 4.1 24.5 - - + -
29V VAL* 4.2 3.1 - - + -
30V LYS 3.3 7.9 - - - +
31V VAL* 4.0 22.7 - - + -
67V LYS* 3.1 41.7 + - + +
70V VAL* 3.8 28.5 - - + -
71V ILE* 3.9 12.0 - - + +
105V ILE* 4.2 11.0 - - + -
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Residues in contact with GLU 11 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9V SER* 5.9 1.8 - - - +
10V VAL* 1.3 76.9 - - - +
12V PHE* 1.3 66.5 + - - +
13V ILE* 3.2 32.6 - - + +
28V ILE 3.4 1.7 - - - +
29V VAL* 3.4 4.5 - - - +
30V LYS* 2.8 53.3 + - + +
51V LYS* 5.8 2.1 + - - -
67V LYS* 4.6 3.8 - - - +
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Residues in contact with PHE 12 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10V VAL* 4.1 9.6 - - + -
11V GLU* 1.3 80.9 - - - +
13V ILE* 1.3 60.9 + - - +
14V PRO* 3.3 11.3 - - - +
27V VAL* 3.9 22.0 - - + -
28V ILE 3.5 3.4 - - - -
29V VAL* 3.9 23.6 - - + -
43V ALA* 4.5 5.2 - - + -
50V MET* 3.5 25.1 - - + -
51V LYS* 3.8 22.5 + - + +
54V SER* 3.6 32.3 + - - +
55V GLU* 4.9 2.5 + - - +
66V ILE* 5.0 2.7 - - + -
67V LYS* 4.9 2.5 - - - +
101V ALA* 3.7 45.5 - - + -
105V ILE* 3.9 20.6 - - + -
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Residues in contact with ILE 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11V GLU* 3.2 38.4 - - + +
12V PHE* 1.3 70.3 - - - +
14V PRO* 1.3 65.9 - - + +
15V VAL* 3.4 6.7 + - + +
27V VAL* 4.0 2.5 - - - +
28V ILE* 2.7 45.9 + - + +
30V LYS* 4.1 18.2 - - + -
378V VAL* 5.1 5.4 - - + -
382V THR* 3.8 30.3 - - + +
386V PHE* 4.0 28.0 - - + -
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Residues in contact with PRO 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12V PHE 3.3 11.9 - - - +
13V ILE* 1.3 86.4 - - + +
15V VAL* 1.3 63.0 + - - +
16V ASN* 4.0 3.8 + - + +
26V THR 3.9 6.1 - - - +
27V VAL* 4.5 2.7 - - + -
47V PRO* 3.8 31.9 - - + +
48V GLU* 3.8 22.0 - - - +
51V LYS* 3.7 26.9 - - + -
382V THR* 3.8 17.5 - - - +
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Residues in contact with VAL 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V ILE* 3.6 10.8 - - + +
14V PRO* 1.3 77.0 - - - +
16V ASN* 1.3 60.3 + - - +
17V VAL* 4.9 2.5 - - + -
24V GLU 4.8 0.2 - - - -
25V ASN* 3.1 8.7 - - - +
26V THR* 3.0 40.6 + - + +
28V ILE* 3.7 28.9 - - + -
47V PRO* 4.6 0.2 - - - +
345V LEU* 4.0 26.5 - - + -
349V LEU* 4.9 4.7 - - + -
377V PHE* 4.9 1.6 - - + -
378V VAL* 5.1 2.7 - - + -
381V VAL* 3.9 25.1 - - + -
382V THR* 4.4 13.5 - - + +
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Residues in contact with ASN 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M GLU* 6.3 0.8 - - - +
14V PRO* 4.0 4.7 + - + +
15V VAL* 1.3 75.3 - - - +
17V VAL* 1.3 75.9 + - - +
18V ALA 4.3 0.2 + - - -
23V SER* 6.0 0.7 - - - -
24V GLU 4.0 2.7 + - - +
25V ASN* 3.7 28.7 + - - +
47V PRO* 3.9 18.3 - - + +
48V GLU* 5.4 7.5 - - - +
381V VAL* 4.7 16.0 + - - +
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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