Contacts of the strand formed by residues 7 - 16 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6M ASN* 1.3 74.5 - - - +
8M VAL* 1.3 62.7 + - - +
9M SER 3.8 11.4 - - - +
10M VAL* 4.4 2.5 - - + -
31M VAL* 3.5 28.3 - - + -
32M THR 3.7 4.3 - - - +
33M ASP* 4.0 1.1 - - - +
70M VAL* 3.6 29.2 - - + +
71M ILE* 3.9 14.7 - - + +
72M GLY* 2.7 29.2 + - - -
73M ARG* 2.9 22.7 + - + +
74M ASP 4.7 0.2 - - - -
75M PRO* 4.0 12.8 - - + -
81M ASN* 5.1 1.1 - - - +
109M LEU* 3.5 29.8 - - + -
112M LEU* 4.0 13.2 - - + -
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Residues in contact with VAL 8 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M ILE* 1.3 75.9 - - - +
9M SER* 1.3 68.7 + - - +
32M THR* 2.7 13.7 + - + +
33M ASP 4.0 4.5 - - - +
34M GLU* 3.5 43.3 - - + -
71M ILE* 3.8 18.5 - - - +
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Residues in contact with SER 9 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M VAL* 1.3 86.0 - - - +
10M VAL* 1.3 70.7 + - - +
11M GLU* 5.6 2.1 - - - +
30M LYS 4.4 0.7 + - - -
31M VAL* 3.3 5.2 - - - +
32M THR* 2.9 45.3 + - - +
71M ILE* 3.5 8.4 - - - +
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Residues in contact with VAL 10 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M ILE* 4.4 0.2 - - + -
9M SER* 1.3 82.9 - - - +
11M GLU* 1.3 65.6 + - - +
12M PHE* 4.0 22.9 - - + -
29M VAL* 4.4 2.0 - - + -
30M LYS 3.3 6.7 - - - +
31M VAL* 4.2 16.4 - - + -
67M LYS* 2.9 51.2 + - + +
70M VAL* 3.8 23.6 - - + -
71M ILE* 3.8 17.8 - - + +
105M ILE* 4.2 12.8 - - + -
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Residues in contact with GLU 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M SER* 5.6 3.1 - - - +
10M VAL* 1.3 76.5 - - - +
12M PHE* 1.3 67.5 + - - +
13M ILE* 3.9 26.4 - - + +
28M ILE 3.5 1.4 - - - +
29M VAL* 3.3 5.0 - - - +
30M LYS* 2.7 57.4 + - + +
51M LYS* 5.5 4.9 + - - +
55M GLU* 5.9 2.2 - - - +
67M LYS* 4.4 4.5 - - - +
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Residues in contact with PHE 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M VAL* 4.0 8.9 + - + -
11M GLU* 1.3 79.2 - - - +
13M ILE* 1.3 61.0 + - - +
14M PRO* 3.5 10.1 - - - +
27M VAL* 3.8 19.1 - - + -
28M ILE 3.5 3.6 - - - -
29M VAL* 3.7 19.5 - - + -
43M ALA* 4.4 7.0 - - + -
50M MET* 3.5 23.1 - - + -
51M LYS* 3.7 24.3 + - - +
54M SER* 3.4 33.1 + - - +
55M GLU* 4.8 2.1 + - - +
66M ILE* 5.1 0.9 - - + -
67M LYS* 4.7 3.6 - - - +
101M ALA* 3.7 44.0 - - + -
105M ILE* 3.7 28.3 - - + -
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Residues in contact with ILE 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M GLU* 4.0 29.4 - - + +
12M PHE* 1.3 73.9 - - - +
14M PRO* 1.3 68.7 - - + +
15M VAL* 3.4 6.9 + - + +
27M VAL* 4.1 1.9 - - - +
28M ILE* 2.7 47.8 + - + +
30M LYS* 4.3 22.0 - - + -
378M VAL* 4.8 7.0 - - + -
382M THR* 4.1 27.8 - - + +
386M PHE* 4.0 28.7 - - + -
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Residues in contact with PRO 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M PHE 3.5 9.2 - - - +
13M ILE* 1.3 85.5 - - + +
15M VAL* 1.3 59.8 + - - +
16M ASN* 4.1 3.5 + - + +
26M THR 3.8 6.3 - - - +
27M VAL* 4.5 3.3 - - + -
47M PRO* 3.6 26.9 - - + +
48M GLU* 3.8 21.3 - - - +
51M LYS* 3.7 35.9 - - + +
382M THR* 3.8 17.7 - - - +
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Residues in contact with VAL 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M ILE* 3.8 8.3 - - + +
14M PRO* 1.3 76.3 - - - +
16M ASN* 1.3 62.5 + - - +
17M VAL* 4.5 2.9 - - + -
25M ASN* 3.2 6.9 - - - +
26M THR* 2.9 49.6 + - + +
28M ILE* 3.7 32.8 - - + -
47M PRO* 4.5 0.2 - - - +
345M LEU* 4.2 24.0 - - + -
349M LEU* 4.8 7.6 - - + -
377M PHE* 5.0 0.4 - - + -
378M VAL* 4.8 4.0 - - + -
381M VAL* 3.9 20.4 - - + -
382M THR* 4.5 13.2 - - + -
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Residues in contact with ASN 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14M PRO* 4.1 3.4 + - + -
15M VAL* 1.3 73.8 - - - +
17M VAL* 1.3 67.9 + - - +
18M ALA 3.9 1.6 + - - -
24M GLU 4.4 0.9 - - - +
25M ASN* 4.0 16.0 + - - +
47M PRO* 3.5 33.7 - - + +
48M GLU* 5.5 9.1 + - - +
381M VAL* 4.8 14.9 + - - +
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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