Contacts of the strand formed by residues 25 - 32 (chain A) in PDB entry 1XZ0
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 GLN 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ILE 3.8 0.6 - - - +
16A ALA* 3.4 0.5 - - - -
17A SER* 3.0 38.0 + - - +
23A TRP* 3.5 30.8 - - + -
24A LYS* 1.3 75.5 - - - +
26A ASN* 1.3 65.6 + - - +
27A LEU* 4.1 31.5 - - + +
78A PHE* 4.1 5.0 - - - -
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Residues in contact with ASN 26 (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 TRP* 3.1 28.4 - - - +
15A ILE 3.1 10.5 - - - +
16A ALA* 4.2 1.3 - - - -
25A GLN* 1.3 80.1 - - - +
27A LEU* 1.3 73.4 + - - +
28A VAL* 5.1 2.1 - - - +
40A TRP* 5.8 3.6 - - - -
42A SER* 5.0 9.7 + - - -
74A THR* 3.9 26.7 + - - -
78A PHE* 4.0 24.0 - - + +
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Residues in contact with LEU 27 (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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13A ILE* 4.1 0.9 - - - +
14A TRP* 3.4 3.8 - - - -
15A ILE* 2.9 48.0 + - + +
25A GLN* 4.1 28.3 - - + +
26A ASN* 1.3 86.6 + - - +
28A VAL* 1.3 63.0 + - - +
54B LEU* 4.4 31.6 - - + +
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Residues in contact with VAL 28 (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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12A VAL* 4.1 7.4 - - + -
13A ILE 3.4 11.0 - - - +
14A TRP* 3.3 31.4 - - + +
26A ASN* 5.1 3.1 - - - +
27A LEU* 1.3 73.8 - - - +
29A SER* 1.3 68.6 + - - +
39A THR* 4.0 4.3 - - - +
40A TRP* 3.3 44.2 + - + +
70A PHE* 4.1 30.5 - - + -
74A THR* 4.1 15.3 - - + -
601A JH0 3.8 13.5 - - + +
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Residues in contact with SER 29 (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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12A VAL* 3.3 6.4 - - - +
13A ILE* 2.9 40.1 + - - +
28A VAL* 1.3 81.6 - - - +
30A GLY* 1.3 58.9 + - - +
31A TRP* 2.9 23.7 + - - -
36A GLN* 3.8 15.3 - - - -
38A HIS 3.4 17.3 - - - -
39A THR* 4.5 3.1 - - - +
601A JH0 4.9 4.0 - - - -
53B ASP* 5.3 1.3 - - - -
54B LEU 5.1 1.9 + - - -
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Residues in contact with GLY 30 (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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10A PHE* 4.2 9.6 - - - -
11A HIS 3.4 7.0 - - - -
12A VAL* 4.3 2.9 - - - -
29A SER* 1.3 73.3 - - - +
31A TRP* 1.3 68.5 + - - -
36A GLN* 3.7 4.2 - - - +
37A THR* 3.0 27.9 + - - -
38A HIS* 3.2 23.5 + - - +
601A JH0 4.7 4.0 - - - +
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Residues in contact with TRP 31 (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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10A PHE* 2.9 26.0 - - - -
11A HIS* 2.7 42.3 + + - +
13A ILE* 3.7 21.5 - - + +
29A SER* 2.9 28.7 + - - -
30A GLY* 1.3 77.7 - - - -
32A LEU* 1.3 55.0 + - - +
33A SER 3.7 14.2 + - - +
34A ASP* 3.2 30.5 - - - -
35A LEU 3.6 3.6 - - - -
36A GLN* 3.3 49.6 - - + -
37A THR* 4.5 0.4 - - - -
52B SER* 6.0 2.5 - - - -
53B ASP* 4.3 11.7 - - + -
54B LEU 4.3 6.7 - - - -
55B SER* 3.5 34.8 - - - -
63B TYR* 4.8 7.6 - + - -
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Residues in contact with LEU 32 (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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8A LEU* 5.5 4.7 - - + -
9A SER 3.6 20.0 - - - +
10A PHE* 4.2 4.7 - - + -
31A TRP* 1.3 70.2 - - - +
33A SER* 1.3 69.0 + - - +
35A LEU* 3.0 31.5 + - + +
37A THR* 4.3 6.8 + - + -
53A TRP* 4.6 9.0 - - + -
170A ILE* 4.8 4.5 - - + -
173A LEU* 3.7 35.0 - - + -
174A LEU* 3.9 18.6 - - + -
181A LEU* 4.0 37.7 - - + -
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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