Contacts of the strand formed by residues 25 - 33 (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 ASN 25 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15M VAL 3.2 15.0 - - - +
16M ASN* 4.0 17.6 + - - +
24M GLU* 1.3 78.4 - - - +
26M THR* 1.3 63.2 + - - +
45M GLY 4.5 2.6 - - - +
47M PRO* 3.6 26.9 - - + +
312M LYS* 3.3 19.8 + - - +
345M LEU* 3.8 12.3 - - - +
59V GLU* 3.4 37.8 + - - +
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Residues in contact with THR 26 (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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15M VAL* 2.9 48.6 + - + +
25M ASN* 1.3 78.0 - - - +
27M VAL* 1.3 74.6 + - - +
28M ILE* 4.3 6.7 - - + -
42M GLU* 2.7 35.5 + - - +
43M ALA 4.4 0.3 + - - -
47M PRO* 3.8 6.0 - - - +
312M LYS* 3.7 17.2 + - - +
313M THR* 4.1 9.9 - - - +
345M LEU* 4.0 11.4 - - + -
349M LEU* 4.2 10.8 - - + -
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Residues in contact with VAL 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M PHE* 3.8 29.8 - - + -
13M ILE 3.6 13.9 - - - +
14M PRO* 4.7 1.8 - - + -
26M THR* 1.3 80.4 + - - +
28M ILE* 1.3 71.3 + - - +
29M VAL* 4.0 2.6 - - + +
42M GLU* 3.1 6.9 - - - -
43M ALA* 3.1 39.1 + - + +
45M GLY 4.2 3.6 - - - +
47M PRO* 3.5 35.7 - - + +
50M MET* 3.9 18.4 - - + -
51M LYS 5.3 0.2 - - - +
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Residues in contact with ILE 28 (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 3.5 2.1 - - - +
12M PHE* 3.5 1.9 - - - -
13M ILE* 2.7 56.4 + - + +
15M VAL* 3.7 24.7 - - + -
26M THR* 4.1 6.5 - - + -
27M VAL* 1.3 72.1 - - - +
29M VAL* 1.3 64.3 + - - +
30M LYS 4.0 1.1 + - - +
40M LEU* 4.0 26.0 - - + -
41M GLY 3.6 9.2 - - - +
42M GLU* 4.6 0.4 - - + +
315M ILE* 3.9 23.3 - - + -
349M LEU* 4.3 6.5 - - + -
373M LEU* 4.3 8.7 - - + -
378M VAL* 4.1 27.6 - - + -
386M PHE* 5.0 3.4 - - + -
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Residues in contact with VAL 29 (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* 4.4 2.0 - - + -
11M GLU 3.3 3.4 - - - +
12M PHE* 3.7 45.8 - - + -
27M VAL* 4.0 9.0 - - + +
28M ILE* 1.3 76.9 - - - +
30M LYS* 1.3 60.2 + - - +
31M VAL* 4.4 10.3 - - + -
40M LEU* 3.5 4.5 - - - -
41M GLY 2.7 39.1 + - - +
43M ALA* 4.1 7.0 - - + +
104M GLY* 3.6 35.0 - - - +
105M ILE* 3.8 15.0 - - + -
108M ALA* 3.7 2.5 - - + +
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Residues in contact with LYS 30 (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* 4.0 1.2 + - - +
10M VAL* 3.3 2.4 - - - -
11M GLU* 2.7 54.7 + - + +
13M ILE* 4.3 17.0 - - + +
28M ILE* 4.0 1.0 - - + -
29M VAL* 1.3 74.3 - - - +
31M VAL* 1.3 63.5 + - - +
32M THR* 3.8 14.6 + - - +
38M TYR* 3.6 43.7 - - + -
39M GLY 3.5 6.1 - - - +
40M LEU* 4.3 8.3 - - + -
386M PHE* 3.8 48.4 + - + +
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Residues in contact with VAL 31 (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* 3.5 43.3 - - + -
9M SER 3.3 4.0 - - - +
10M VAL* 4.2 15.7 - - + -
29M VAL* 4.4 9.9 - - + -
30M LYS* 1.3 76.5 - - - +
32M THR* 1.3 63.6 + - - +
38M TYR* 3.1 4.0 - - - -
39M GLY 3.0 31.4 + - - +
70M VAL* 5.4 0.2 - - + -
105M ILE* 4.5 12.3 - - + -
108M ALA* 3.7 24.0 - - + -
109M LEU* 4.1 7.9 - - + -
112M LEU* 3.8 13.2 - - + +
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Residues in contact with THR 32 (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* 3.7 3.1 - - - -
8M VAL* 2.7 33.9 + - + +
9M SER* 2.9 28.7 + - - +
30M LYS* 3.8 17.0 - - - +
31M VAL* 1.3 74.6 - - - +
33M ASP* 1.3 65.1 + - - +
36M GLY* 3.8 19.5 - - - +
37M VAL 3.3 11.4 - - - +
38M TYR* 3.6 11.1 - - + +
112M LEU* 4.8 1.1 - - - -
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Residues in contact with ASP 33 (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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5M ALA* 3.8 8.5 - - + +
6M ASN 3.1 18.6 - - - +
7M ILE* 4.0 1.1 - - - +
8M VAL* 3.8 7.9 - - - +
31M VAL 4.2 0.6 + - - -
32M THR* 1.3 80.1 - - - +
34M GLU* 1.3 65.6 + - - +
35M ASN* 2.8 19.0 + - - +
36M GLY 3.2 8.3 + - - -
37M VAL* 2.8 46.4 + - - +
112M LEU* 3.8 9.0 - - + +
116M GLN* 2.6 37.5 + - - +
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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