Contacts of the strand formed by residues 15 - 20 (chain A) in PDB entry 2XWA
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 MET 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ARG* 2.9 20.1 + - + +
13A PRO 3.3 2.8 - - - +
14A TYR* 1.3 83.0 - - - +
16A ALA* 1.3 75.1 + - - +
27A GLY* 4.3 9.0 - - - -
28A GLY 3.9 3.8 - - - +
54A LEU 4.3 2.9 - - - +
55A LEU* 4.0 12.6 - - - +
56A GLY 4.6 4.5 + - - -
57A ALA* 5.3 6.3 + - - +
126A ALA* 3.3 35.7 - - + +
127A GLY* 4.0 9.4 - - - -
128A TRP* 4.0 16.3 - - + -
141A LEU* 3.7 28.3 - - + -
186A PRO* 3.5 35.2 - - + -
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TYR 4.4 2.0 - - - +
15A MET* 1.3 76.0 - - - +
17A SER* 1.3 60.6 + - - +
18A VAL 3.9 0.4 - - - +
27A GLY* 3.5 5.4 - - - -
28A GLY* 2.9 46.1 + - - +
29A VAL* 4.2 0.7 - - - +
36A VAL* 3.9 19.7 - - + -
53A VAL* 4.2 6.5 - - + -
54A LEU 3.7 3.8 - - - -
55A LEU* 3.8 18.8 - - + -
128A TRP* 3.6 10.1 - - - -
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 1.3 72.3 - - - +
18A VAL* 1.3 61.5 + - - +
19A GLN* 3.1 29.9 + - - +
24A HIS* 2.7 26.6 + - - +
26A CYS 3.7 3.6 - - - -
53A VAL* 3.3 3.4 - - - -
54A LEU* 2.8 46.2 + - - -
60A LEU* 4.0 6.2 - - - +
128A TRP* 3.8 15.8 - - - -
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 5.0 0.2 - - + -
17A SER* 1.3 73.1 + - - +
19A GLN* 1.3 63.6 + - - +
25A LEU* 2.9 31.9 + - + -
26A CYS* 2.7 32.8 + - + +
27A GLY 3.6 20.9 - - - +
28A GLY* 4.3 5.8 - - - -
36A VAL* 4.4 7.4 - - + -
38A SER* 3.7 11.9 - - - +
42A CYS* 5.5 2.2 - - + -
43A LEU* 5.8 2.2 - - + -
51A VAL* 4.4 12.3 - - + -
52A GLN 3.8 6.7 - - - +
53A VAL* 4.5 3.6 - - + -
91A LEU* 5.2 5.4 - - + -
93A LEU* 3.9 31.0 - - + -
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Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 3.1 35.0 + - - +
18A VAL* 1.3 74.8 - - - +
20A LEU* 1.3 60.3 + - - +
21A ASN 4.2 0.2 - - - -
22A GLY* 3.7 22.1 + - - +
23A ALA 3.2 9.4 - - - +
24A HIS* 4.2 12.2 - - - +
25A LEU* 4.7 2.0 - - - -
50A LYS 3.6 0.2 - - - +
51A VAL* 3.3 9.0 - - - +
52A GLN* 2.7 48.5 + - + +
54A LEU* 3.8 30.6 - - - +
60A LEU* 4.1 10.5 + - - +
69A LEU* 4.2 12.7 - - - +
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLN* 1.3 72.1 - - - +
21A ASN* 1.3 82.7 + - - +
22A GLY 3.2 1.1 - - - -
23A ALA* 2.9 22.9 + - - +
25A LEU* 4.0 37.3 - - + +
45A ASP* 5.9 4.5 - - - +
46A ALA 5.3 2.7 - - - +
47A ALA* 3.9 28.7 - - + -
49A GLY* 4.1 15.3 - - - -
50A LYS 3.3 4.0 - - - +
51A VAL* 4.1 15.9 - - + -
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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