Contacts of the strand formed by residues 7 - 17 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6T ASN* 1.3 73.4 - - - +
8T VAL* 1.3 64.3 + - - +
9T SER 3.7 10.3 - - - +
10T VAL* 4.2 2.9 - - + -
31T VAL* 3.6 27.6 - - + -
32T THR 3.6 5.4 - - - +
33T ASP* 4.2 1.3 - - - +
70T VAL* 3.3 36.1 - - + +
71T ILE* 3.7 19.1 - - + +
72T GLY* 2.7 28.4 + - - -
73T ARG* 3.0 20.5 + - + +
74T ASP 5.0 0.2 - - - -
75T PRO* 4.4 9.9 - - + -
81T ASN* 5.3 1.1 - - - +
109T LEU* 3.6 26.5 - - + -
112T LEU* 4.2 12.1 - - + -
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Residues in contact with VAL 8 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6T ASN* 3.7 0.4 + - + -
7T ILE* 1.3 77.7 - - - +
9T SER* 1.3 64.3 + - - +
32T THR* 2.7 15.8 + - + +
33T ASP 4.4 4.9 - - - +
34T GLU* 3.8 35.4 - - + -
71T ILE* 3.7 19.6 - - - +
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Residues in contact with SER 9 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7T ILE* 3.7 1.0 - - - +
8T VAL* 1.3 87.8 - - - +
10T VAL* 1.3 71.6 - - - +
11T GLU* 4.5 13.5 + - - -
30T LYS 4.3 0.2 - - - -
31T VAL* 3.4 4.2 - - - +
32T THR* 3.0 48.5 + - - -
71T ILE* 3.8 3.6 - - - -
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Residues in contact with VAL 10 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7T ILE* 4.2 0.4 - - + -
9T SER* 1.3 80.4 - - - +
11T GLU* 1.3 64.8 - - - +
12T PHE* 4.0 26.2 - - + -
29T VAL* 4.2 13.2 - - + -
30T LYS 3.4 3.4 - - - -
31T VAL* 4.1 16.8 - - + -
67T LYS* 2.9 48.4 + - + +
70T VAL* 3.9 22.4 - - + -
71T ILE* 3.9 17.8 - - + +
105T ILE* 4.2 9.2 - - + -
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Residues in contact with GLU 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9T SER* 4.5 15.0 + - - +
10T VAL* 1.3 82.2 - - - +
12T PHE* 1.3 63.0 + - - +
13T ILE* 3.7 21.5 + - + +
28T ILE 3.4 2.1 - - - +
29T VAL* 3.3 4.7 - - - +
30T LYS* 2.8 64.7 + - + +
32T THR* 4.5 1.2 + - - -
67T LYS* 4.5 2.9 - - - +
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Residues in contact with PHE 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T VAL* 4.0 12.1 + - + -
11T GLU* 1.3 75.0 - - - +
13T ILE* 1.3 61.6 + - - +
14T PRO* 3.4 1.2 - - - +
27T VAL* 3.7 21.3 - - + -
28T ILE 3.5 2.7 - - - -
29T VAL* 3.9 23.6 - - + -
43T ALA* 4.3 7.0 - - + -
50T MET* 3.6 23.6 - - + -
51T LYS* 3.3 33.1 - - + +
54T SER* 3.6 31.9 + - - +
55T GLU* 5.3 1.1 + - - +
66T ILE* 5.0 2.0 - - + -
67T LYS* 4.9 3.1 - - - +
101T ALA* 3.7 44.9 - - + -
105T ILE* 3.9 19.1 - - + -
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Residues in contact with ILE 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T GLU* 4.2 21.1 - - + +
12T PHE* 1.3 74.3 - - - +
14T PRO* 1.3 71.5 - - + +
15T VAL* 3.6 4.9 - - + +
27T VAL* 3.9 2.3 - - - +
28T ILE* 2.6 51.0 + - + +
30T LYS* 4.3 28.0 - - + +
382T THR* 3.2 39.7 - - + +
384T HIS* 5.5 4.5 - - + -
386T PHE* 4.4 21.3 - - + -
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Residues in contact with PRO 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T PHE 3.4 7.8 - - - +
13T ILE* 1.3 92.0 - - + +
15T VAL* 1.3 62.5 - - - +
16T ASN* 4.0 5.1 + - - +
26T THR 3.9 4.7 - - - +
27T VAL* 4.6 3.8 - - + -
47T PRO* 3.7 23.3 - - + +
48T GLU* 4.0 20.4 - - - +
51T LYS* 3.6 37.9 - - + -
381T VAL 4.5 7.4 - - - +
382T THR* 4.7 5.4 - - - +
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Residues in contact with VAL 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T ILE* 3.6 11.9 - - + +
14T PRO* 1.3 79.1 - - - +
16T ASN* 1.3 55.2 + - - +
17T VAL* 4.1 8.1 - - + -
25T ASN* 2.6 33.4 - - - +
26T THR* 2.9 29.0 + - + +
28T ILE* 3.9 27.1 - - + -
47T PRO* 4.2 1.4 - - - +
345T LEU* 4.0 27.6 - - + -
349T LEU* 5.6 4.5 - - + -
378T VAL* 6.0 0.2 - - + -
381T VAL* 4.2 19.3 - - + +
382T THR* 4.7 10.8 - - - +
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Residues in contact with ASN 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14T PRO* 4.0 11.9 + - - +
15T VAL* 1.3 74.0 - - - +
17T VAL* 1.3 65.1 + - - +
18T ALA 4.2 0.9 - - - -
25T ASN* 3.6 19.3 + - - +
47T PRO* 4.2 11.5 - - - +
48T GLU* 3.5 28.5 + - - +
381T VAL* 5.0 10.5 + - - +
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Residues in contact with VAL 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15T VAL* 3.9 11.8 + - + -
16T ASN* 1.3 79.8 - - - +
18T ALA* 1.3 67.0 + - - +
23T SER 5.0 0.4 - - - -
24T GLU* 2.5 52.7 + - + +
25T ASN* 4.1 1.4 - - - +
344T THR* 4.1 27.8 - - + +
345T LEU* 3.7 24.7 - - + -
377T PHE* 5.3 1.6 - - + -
381T VAL* 4.3 17.9 - - + -
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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