Contacts of the strand formed by residues 123 - 128 (chain A) in PDB entry 1X2W
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 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU 2.9 12.4 - - - +
20A TYR* 3.9 1.3 - - - -
21A LYS 2.9 18.4 + - - +
64A SER* 3.6 13.9 - - - -
65A TYR* 3.1 24.4 + - - +
67A TRP* 3.5 25.0 - - + +
117A ILE* 3.8 8.5 - - - +
121A GLN* 2.9 42.5 + - - +
122A GLN* 1.3 80.6 + - - +
124A PRO* 1.3 75.3 - - + +
125A PHE* 3.6 4.9 - - - -
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Residues in contact with PRO 124 (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 PHE 3.3 13.2 - - - +
18A LYS* 3.9 9.4 - - + -
19A LEU 2.9 14.8 - - - +
20A TYR* 3.9 11.2 - - + -
59A ILE* 3.8 27.8 - - + -
62A THR* 4.1 11.0 - - + +
64A SER* 3.9 12.8 - - - -
65A TYR 3.3 17.5 - - - +
66A VAL* 3.6 7.4 - - + -
67A TRP* 3.2 18.5 + - - -
123A ASN* 1.3 88.6 - - + +
125A PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 125 (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 PRO* 3.5 0.2 - - - +
17A PHE* 2.8 52.8 + + + +
19A LEU* 3.3 31.2 - - + -
21A LYS* 4.1 19.1 - - + -
26A ALA* 4.0 13.5 - - + -
29A PHE* 3.5 35.2 - + - -
30A CYS* 3.7 18.4 - - - -
39A LEU* 3.6 19.3 - - + -
59A ILE* 3.7 2.5 - - - +
66A VAL* 3.9 11.4 - - - +
67A TRP* 3.6 9.6 - - + +
123A ASN 3.6 6.3 - - - -
124A PRO* 1.3 81.4 - - - +
126A VAL* 1.3 70.8 + - - +
127A CYS* 3.8 5.2 - - - -
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 4.3 5.6 - - + -
15A LYS 3.5 9.2 - - - +
16A PRO* 3.6 20.4 - - + -
30A CYS* 4.3 0.9 - - - -
39A LEU* 3.7 6.6 - - - +
40A VAL* 2.9 49.4 + - + +
51A VAL* 5.1 4.7 - - + -
54A LEU* 4.2 19.7 - - + -
55A VAL* 4.1 16.6 - - + -
59A ILE* 3.9 10.5 - - + -
66A VAL* 4.5 3.4 - - + -
67A TRP 4.1 4.6 + - - +
125A PHE* 1.3 82.3 - - - +
127A CYS* 1.3 75.6 + - - +
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Residues in contact with CYS 127 (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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6A TRP* 4.2 15.7 - - + -
14A TYR* 3.3 4.7 - - - -
15A LYS 2.9 34.0 + - - +
17A PHE* 3.6 28.7 - - + -
30A CYS* 2.0 53.8 - - + +
33A GLN* 4.3 4.3 - - - -
37A GLY* 5.9 0.2 - - - -
38A HIS 3.3 6.7 - - - +
125A PHE* 3.8 4.7 - - - -
126A VAL* 1.3 79.7 - - - +
128A GLU* 1.3 60.8 + - - +
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Residues in contact with GLU 128 (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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6A TRP* 4.4 1.3 - - - -
12A HIS* 3.0 35.4 + - + +
13A CYS 3.2 8.3 - - - +
14A TYR* 3.5 32.0 + - + -
36A GLY 3.8 2.9 - - - +
37A GLY* 3.7 1.2 - - - -
38A HIS* 2.8 34.0 + - - +
39A LEU 4.9 0.8 - - - +
40A VAL* 4.0 9.4 - - - -
41A SER* 3.1 39.9 + - - +
43A GLU* 5.3 0.7 - - - +
47A GLU* 3.8 3.6 - - - +
127A CYS* 1.3 76.8 - - - +
129A ALA* 1.3 68.5 + - - +
81B ASN* 5.0 5.2 + - - -
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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