Contacts of the strand formed by residues 25 - 33 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59Q GLU* 3.0 36.2 + - - +
15U VAL 3.0 19.5 - - - +
16U ASN* 3.3 28.1 + - - +
23U SER* 4.0 11.1 - - - -
24U GLU* 1.3 77.0 - - - +
26U THR* 1.3 62.4 + - - +
45U GLY 4.9 1.9 - - - +
47U PRO* 3.8 18.6 - - + +
312U LYS* 3.5 18.9 + - - +
345U LEU* 3.7 10.4 - - - +
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Residues in contact with THR 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U VAL* 2.9 47.1 + - + +
25U ASN* 1.3 79.7 + - - +
27U VAL* 1.3 72.2 + - - +
28U ILE* 4.4 2.9 - - + +
42U GLU* 2.6 35.5 + - - +
43U ALA 4.3 0.9 + - - -
45U GLY 5.6 0.9 - - - -
47U PRO* 3.6 9.6 - - - +
312U LYS* 3.6 18.1 + - - +
313U THR* 4.3 1.3 - - - +
345U LEU* 4.1 12.8 - - + -
349U LEU* 4.3 15.9 - - + -
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Residues in contact with VAL 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U PHE* 3.7 43.3 - - + -
13U ILE 3.5 11.9 - - - +
14U PRO* 4.5 1.8 - - + -
26U THR* 1.3 79.6 + - - +
28U ILE* 1.3 62.9 + - - +
29U VAL* 3.5 1.5 + - + -
42U GLU* 3.2 8.0 - - - +
43U ALA* 3.1 38.6 + - + +
45U GLY 4.3 2.7 - - - +
47U PRO* 3.5 37.5 - - + +
50U MET* 3.9 18.4 - - + -
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Residues in contact with ILE 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U GLU 3.4 1.9 - - - +
12U PHE* 3.6 1.4 - - - -
13U ILE* 2.7 55.1 + - + +
15U VAL* 3.9 25.6 - - + -
26U THR* 4.5 5.6 - - + -
27U VAL* 1.3 72.0 - - - +
29U VAL* 1.3 71.1 + - - +
30U LYS 3.9 0.8 + - - +
40U LEU* 4.1 20.0 - - + -
41U GLY 3.7 7.6 - - - +
42U GLU* 4.6 1.1 - - - -
315U ILE* 4.0 24.2 - - + -
349U LEU* 4.4 15.3 - - + -
373U LEU* 4.5 8.7 - - + -
378U VAL* 4.4 18.8 - - + -
386U PHE* 5.4 2.9 - - + -
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Residues in contact with VAL 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10U VAL* 4.2 6.5 - - + -
11U GLU 3.4 4.9 - - - +
12U PHE* 3.8 28.9 - - + -
27U VAL* 4.0 9.4 - - + +
28U ILE* 1.3 78.0 - - - +
30U LYS* 1.3 61.2 + - - +
31U VAL* 4.4 6.1 - - + -
39U GLY 3.6 0.9 - - - +
40U LEU* 3.3 7.6 - - - -
41U GLY 2.8 35.0 + - - +
43U ALA* 4.0 7.6 - - + +
104U GLY* 3.8 27.8 - - - +
105U ILE* 3.7 33.7 - - + -
108U ALA* 3.9 0.7 - - + +
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Residues in contact with LYS 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U SER 3.8 1.0 - - - +
10U VAL* 3.3 3.1 - - - -
11U GLU* 2.8 58.5 + - + +
13U ILE* 4.2 13.7 - - + -
28U ILE* 3.9 0.6 + - + -
29U VAL* 1.3 73.2 - - - +
31U VAL* 1.3 62.2 - - - +
32U THR* 4.1 13.9 + - - +
38U TYR* 3.8 34.7 - - + -
39U GLY 3.6 2.0 - - - -
40U LEU* 3.8 18.6 - - + -
386U PHE* 3.8 53.4 + - + +
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Residues in contact with VAL 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7U ILE* 3.5 29.4 - - + -
9U SER 3.4 4.0 - - - +
10U VAL* 4.3 14.1 - - + -
29U VAL* 4.4 9.9 - - + -
30U LYS* 1.3 76.7 - - - +
32U THR* 1.3 63.0 + - - +
38U TYR* 2.9 3.4 - - - -
39U GLY 2.8 36.1 + - - +
70U VAL* 6.0 0.2 - - + -
105U ILE* 4.4 7.2 - - + -
108U ALA* 3.7 24.0 - - + +
109U LEU* 4.0 19.1 - - + -
112U LEU* 3.6 21.9 - - + +
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Residues in contact with THR 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7U ILE* 3.8 2.3 - - - +
8U VAL* 2.9 26.6 + - + -
9U SER* 3.0 28.8 + - - +
11U GLU* 5.7 0.3 + - - -
30U LYS* 4.1 17.4 + - - +
31U VAL* 1.3 75.5 - - - +
33U ASP* 1.3 72.2 + - - +
36U GLY* 3.8 19.5 - - - +
37U VAL 3.2 11.2 - - - +
38U TYR* 3.7 10.6 - - + +
112U LEU* 4.6 2.7 - - - -
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Residues in contact with ASP 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U ALA* 3.6 10.2 - - + +
6U ASN 3.4 15.0 - - - +
7U ILE* 4.3 0.9 - - - +
8U VAL* 4.0 8.7 - - - +
31U VAL 4.3 0.2 + - - -
32U THR* 1.3 81.7 - - - +
34U GLU* 1.3 63.4 + - - +
35U ASN* 2.6 30.8 + - - +
36U GLY* 3.0 17.7 + - - -
37U VAL* 2.6 39.4 + - - +
112U LEU* 4.1 6.4 - - + +
116U GLN* 3.2 35.9 + - - +
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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