Contacts of the strand formed by residues 18 - 26 (chain Y) in PDB entry 2XB2
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 GLY 18 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13Y HIS* 4.4 0.9 + - - -
14Y LYS* 3.4 3.5 - - - -
15Y GLY 3.1 30.7 + - - -
16Y LYS 3.5 1.2 - - - -
17Y PHE* 1.3 81.5 - - - +
19Y HIS* 1.3 59.8 - - - -
20Y GLU* 3.3 7.8 + - - +
39Y ASN* 4.8 7.6 - - - -
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Residues in contact with HIS 19 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Y TYR* 2.6 32.9 + + - -
13Y HIS 3.3 18.6 - - - -
14Y LYS* 3.5 33.7 + - + -
17Y PHE 5.0 0.4 - - - -
18Y GLY* 1.3 68.1 - - - -
20Y GLU* 1.3 59.3 + - - +
21Y PHE* 3.3 35.2 - + - -
37Y ASN* 2.8 30.0 + - - +
38Y SER* 5.3 0.2 - - - -
39Y ASN* 5.1 2.2 + - - -
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Residues in contact with GLU 20 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358X ARG* 2.6 42.9 + - - -
391X ASP 5.5 0.3 - - - +
394X GLN* 3.2 9.4 + - - +
395X TYR* 4.0 3.6 - - - +
12Y GLY* 3.0 2.4 - - - -
13Y HIS* 2.9 66.3 + - + +
17Y PHE* 3.5 29.9 - - + +
18Y GLY 3.3 1.9 + - - +
19Y HIS* 1.3 69.5 - - - +
21Y PHE* 1.3 61.5 + - - +
37Y ASN 3.3 6.5 - - - +
38Y SER* 2.6 31.5 + - - +
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Residues in contact with PHE 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394X GLN* 3.2 10.9 - - - +
10Y TYR* 3.3 39.0 - + + +
11Y VAL 3.2 4.0 - - - +
12Y GLY* 3.7 1.8 - - - -
19Y HIS* 3.3 34.5 - + - +
20Y GLU* 1.3 75.0 - - - +
22Y LEU* 1.3 61.9 + - - +
23Y GLU* 4.0 25.4 - - + -
35Y ALA* 4.3 10.5 - - + -
36Y ASN* 3.5 3.1 - - - -
37Y ASN* 2.9 58.4 + - + +
45Y MET* 3.7 24.0 - - + -
47Y ARG* 5.5 0.9 - - - -
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Residues in contact with LEU 22 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394X GLN* 4.0 17.7 - - + +
397X SER* 3.8 11.7 - - - +
9Y TYR* 4.4 4.3 - - + -
10Y TYR* 3.4 1.4 - - - -
11Y VAL* 2.8 51.9 + - + +
21Y PHE* 1.3 75.0 - - - +
23Y GLU* 1.3 69.8 + - - +
24Y PHE* 4.2 23.8 - - + -
34Y TYR* 3.5 33.7 - - + -
35Y ALA 3.6 4.9 - - - +
36Y ASN* 4.0 10.5 - - + +
130Y LYS* 4.4 11.2 - - - +
134Y PHE* 4.6 13.2 - - + -
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Residues in contact with GLU 23 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y ARG* 3.5 29.3 + - + -
9Y TYR 3.2 15.3 - - - +
10Y TYR* 4.1 14.8 - - + +
21Y PHE* 4.0 22.5 - - + -
22Y LEU* 1.3 80.4 - - - +
24Y PHE* 1.3 70.2 + - - +
25Y GLU* 5.8 1.6 - - + -
33Y ARG 4.0 0.3 - - - +
34Y TYR* 3.5 1.7 - - - -
35Y ALA* 2.7 46.8 + - + +
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Residues in contact with PHE 24 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y LEU* 5.2 4.5 - - + -
8Y ARG* 3.5 2.2 - - - +
9Y TYR* 3.0 71.6 + + + +
22Y LEU* 4.2 19.5 - - + -
23Y GLU* 1.3 79.9 - - - +
25Y GLU* 1.3 60.0 + - - +
26Y PHE* 4.3 13.2 - + - -
32Y LEU* 4.4 3.4 - - + -
33Y ARG 3.1 10.1 - - - +
34Y TYR* 4.2 8.5 - + + -
129Y LEU* 4.3 26.5 - - + -
130Y LYS* 4.4 11.7 - - + -
133Y VAL* 3.6 50.0 - - + -
134Y PHE* 5.7 1.6 - + - -
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Residues in contact with GLU 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y TYR* 2.8 42.7 + - + +
7Y LEU 3.4 5.2 - - - +
8Y ARG* 4.2 12.2 - - + +
23Y GLU* 5.8 1.8 - - + -
24Y PHE* 1.3 74.8 - - - +
26Y PHE* 1.3 66.7 + - - +
27Y ARG* 3.3 26.8 + - + +
31Y LYS 3.3 3.3 - - - +
32Y LEU* 3.1 5.6 - - - +
33Y ARG* 2.7 74.8 + - + +
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Residues in contact with PHE 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Y PHE* 4.2 0.8 - - + +
6Y TYR* 3.4 5.8 - - - -
7Y LEU* 2.6 47.0 + - + +
24Y PHE* 4.3 7.4 - + - -
25Y GLU* 1.3 74.7 - - - +
27Y ARG* 1.3 64.1 + - - +
31Y LYS 3.7 2.9 - - - -
32Y LEU* 3.5 44.4 - - + -
52Y VAL* 4.5 12.1 - - + -
56Y VAL* 4.9 3.8 - - + -
57Y MET* 4.3 17.4 - - + +
60Y LEU* 3.5 39.7 - - + -
129Y LEU* 6.1 0.4 - - + -
132Y LEU* 4.6 5.2 - - + -
133Y VAL* 3.5 28.7 - - + -
136Y LEU* 4.2 14.1 - - + -
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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