Contacts of the strand formed by residues 25 - 33 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C VAL 2.9 19.5 - - - +
16C ASN* 3.5 21.2 + - - +
24C GLU* 1.3 79.3 - - - +
26C THR* 1.3 62.5 + - - +
45C GLY 5.0 1.2 - - - +
47C PRO* 3.7 21.7 - - + +
312C LYS* 3.3 17.0 + - - +
345C LEU* 3.6 14.6 - - - +
59F GLU* 3.5 37.5 + - - +
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Residues in contact with THR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 3.0 45.6 + - + +
25C ASN* 1.3 78.2 - - - +
27C VAL* 1.3 70.4 + - - +
28C ILE* 4.0 6.3 - - + -
42C GLU* 2.6 37.1 + - - +
43C ALA 4.3 0.2 + - - -
47C PRO* 3.5 11.7 - - - +
312C LYS* 3.6 18.2 + - - +
313C THR* 4.1 13.2 - - - +
345C LEU* 4.2 5.4 - - + -
349C LEU* 4.2 11.2 - - + -
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 3.8 40.2 - - + -
13C ILE 3.6 11.9 - - - +
14C PRO* 4.8 0.9 - - + -
26C THR* 1.3 82.1 + - - +
28C ILE* 1.3 62.6 + - - +
29C VAL* 3.6 2.4 + - + -
42C GLU* 3.0 5.0 - - - -
43C ALA* 3.0 40.7 + - + +
45C GLY 4.2 2.7 - - - +
47C PRO* 3.3 38.8 - - + +
50C MET* 3.9 17.0 - - + -
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Residues in contact with ILE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLU 3.4 2.8 - - - +
12C PHE* 3.6 0.7 - - - -
13C ILE* 2.8 54.1 + - + +
15C VAL* 3.6 26.2 - - + -
26C THR* 4.0 5.6 - - + -
27C VAL* 1.3 71.2 - - - +
29C VAL* 1.3 64.7 + - - +
30C LYS 3.9 0.2 + - - -
40C LEU* 4.0 27.1 - - + -
41C GLY 3.5 9.9 - - - +
42C GLU* 4.4 0.7 - - - +
315C ILE* 3.7 21.3 - - + -
349C LEU* 4.4 9.0 - - + -
373C LEU* 4.6 7.2 - - + -
378C VAL* 4.3 28.5 - - + -
386C PHE* 5.0 3.4 - - + -
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 4.3 2.5 - - + -
11C GLU 3.5 3.8 - - - +
12C PHE* 3.8 43.5 - - + -
27C VAL 4.1 9.4 - - - +
28C ILE* 1.3 76.5 - - - +
30C LYS* 1.3 61.2 + - - +
31C VAL* 4.1 12.1 - - + -
39C GLY 3.5 0.7 - - - +
40C LEU* 3.3 8.3 - - - +
41C GLY 2.7 33.8 + - - +
43C ALA 4.1 3.1 - - - +
104C GLY* 3.8 25.8 - - - +
105C ILE* 3.8 27.1 - - + -
108C ALA* 3.8 1.5 - - + +
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Residues in contact with LYS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C SER* 4.0 0.7 + - - +
10C VAL* 3.3 3.8 - - - -
11C GLU* 2.8 56.2 + - + +
13C ILE* 4.1 16.4 - - + -
28C ILE* 3.9 0.4 + - + -
29C VAL* 1.3 73.6 - - - +
31C VAL* 1.3 61.1 + - - +
32C THR* 4.0 17.2 + - - +
38C TYR* 3.7 42.3 - - + -
39C GLY 3.5 2.9 - - - -
40C LEU* 4.2 7.4 - - + -
386C PHE* 3.6 48.1 + - + -
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 3.5 40.8 - - + -
9C SER 3.4 4.9 - - - +
10C VAL* 4.1 15.5 - - + -
29C VAL* 4.2 9.9 - - + -
30C LYS* 1.3 76.2 - - - +
32C THR* 1.3 63.8 + - - +
38C TYR* 3.0 2.7 - - - -
39C GLY 2.8 34.8 + - - +
105C ILE* 4.5 5.6 - - + -
108C ALA* 3.7 25.8 - - + +
109C LEU* 3.9 19.7 - - + -
112C LEU* 3.8 8.9 - - + +
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 3.7 4.3 - - - +
8C VAL* 2.8 25.2 + - + -
9C SER* 3.1 29.5 + - - +
30C LYS* 4.0 17.6 + - - +
31C VAL* 1.3 75.6 - - - +
33C ASP* 1.3 70.2 + - - +
36C GLY* 3.8 19.3 - - - +
37C VAL 3.4 9.4 - - - +
38C TYR* 3.8 11.3 - - + +
112C LEU* 4.7 1.6 - - - -
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Residues in contact with ASP 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ALA* 3.9 8.6 - - - +
6C ASN 3.3 17.3 - - - +
7C ILE* 4.2 0.7 - - - +
8C VAL* 4.1 7.6 - - - +
31C VAL 4.3 0.2 + - - -
32C THR* 1.3 78.6 - - - +
34C GLU* 1.3 60.6 + - - +
35C ASN* 3.0 13.4 + - - -
36C GLY* 2.9 19.6 + - - -
37C VAL* 2.7 54.4 + - - +
112C LEU* 3.9 6.8 - - + +
116C GLN* 2.7 37.3 + - - +
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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