Contacts of the strand formed by residues 21 - 26 (chain W) in PDB entry 5LMQ
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 THR 21 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1410A G 6.5 1.1 - - - -
44L THR* 5.6 6.7 - - + -
17W LEU* 3.0 38.8 + - + +
18W PRO* 2.8 20.0 + - - +
19W ASN* 3.8 13.3 + - - +
20W ALA* 1.3 71.2 - - - +
22W PHE* 1.3 67.9 - - - +
33W LEU* 4.8 18.4 - - + -
34W ALA 3.9 14.8 - - - +
35W TYR* 4.0 14.4 - - + +
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Residues in contact with PHE 22 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1493A A 4.2 11.0 - - - -
13W VAL* 4.2 7.6 - - + -
15W GLU 3.3 20.2 - - - +
16W ALA* 3.4 22.2 - - + -
17W LEU* 4.2 7.9 - - - -
20W ALA* 3.5 34.8 - - + -
21W THR* 1.3 87.4 - - - +
23W ARG* 1.3 62.1 + - - +
24W VAL* 3.4 18.8 + - + +
32W ILE 3.5 0.2 - - - +
33W LEU* 5.0 2.0 - - - -
34W ALA* 2.8 38.6 + - - +
47W ILE* 3.6 49.4 - - + -
49W PRO* 5.5 0.7 - - + -
67W ILE* 3.4 19.7 - - + -
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Residues in contact with ARG 23 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409A C 4.5 25.5 + - - -
1410A G 4.6 5.9 + - - -
13W VAL* 3.8 0.2 - - - +
14W THR* 3.3 5.5 + - + -
15W GLU* 3.0 57.7 + - + +
17W LEU* 4.2 15.1 - - + +
22W PHE* 1.3 69.9 - - - +
24W VAL* 1.3 58.5 + - - +
31W GLU* 3.4 43.4 + - + +
32W ILE 3.9 7.5 - - - -
33W LEU* 2.2 53.0 - - - +
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Residues in contact with VAL 24 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W GLY* 3.6 34.8 - - - +
12W VAL 3.6 7.4 - - - +
13W VAL* 3.9 14.1 - - + -
14W THR 3.8 1.6 - - - +
22W PHE* 3.4 26.3 + - + +
23W ARG* 1.3 79.8 - - - +
25W LYS* 1.3 59.3 + - - +
26W LEU* 3.6 6.5 + - + +
30W PRO 3.8 1.0 - - - +
31W GLU* 3.3 19.1 - - - -
32W ILE* 3.7 8.3 + - + +
34W ALA* 4.4 10.8 - - + -
53W VAL* 4.1 5.6 - - + -
55W VAL* 3.6 26.5 - - + -
67W ILE* 4.9 3.1 - - + -
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Residues in contact with LYS 25 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W GLY* 4.1 0.2 - - - -
12W VAL* 2.8 47.3 + - + +
14W THR* 3.1 17.6 + - - +
24W VAL* 1.3 70.1 - - - +
26W LEU* 1.3 62.1 + - - +
29W GLY 3.1 25.6 - - - +
30W PRO* 3.8 11.2 - - - +
31W GLU* 3.8 20.1 + - + +
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Residues in contact with LEU 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W THR* 3.9 13.2 - - + +
10W GLU 3.3 25.8 - - - +
11W GLY* 3.7 3.1 - - - -
12W VAL* 5.5 1.0 - - - +
24W VAL 4.1 5.6 - - - +
25W LYS* 1.3 82.1 - - - +
27W ASP* 1.3 63.7 + - - +
28W SER* 3.2 15.7 - - - +
29W GLY* 3.7 14.0 + - - +
30W PRO* 3.0 40.6 + - + +
32W ILE* 3.8 19.7 - - + -
55W VAL* 3.9 26.2 - - + -
57W ILE* 4.1 11.7 - - + -
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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