Contacts of the strand formed by residues 137 - 142 (chain B) in PDB entry 1XSK
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 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B HIS* 2.8 25.6 + - - +
19B PRO* 3.6 25.4 - - - +
55B LEU* 5.2 2.8 - - - +
69B ILE* 4.6 11.6 - - + +
118B TRP* 4.9 9.1 + - - +
120B LEU* 4.4 9.9 - - - +
132B SER* 3.6 15.2 + - - -
133B GLN 4.6 1.7 - - - +
135B LYS 3.4 3.5 + - - -
136B ASN* 1.3 77.4 + - - +
138B GLY* 1.3 60.6 + - - +
151B PHE* 3.1 23.9 - - - +
152B GLU* 3.1 32.8 + - + +
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Residues in contact with GLY 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE 3.4 9.6 - - - -
19B PRO* 4.1 4.3 - - - -
53B PHE* 4.1 11.4 - - - -
69B ILE* 4.5 5.3 - - - +
137B ASN* 1.3 81.0 - - - +
139B TYR* 1.3 60.6 + - - -
150B MET* 3.3 13.6 - - - +
151B PHE* 3.0 35.9 + - - -
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Residues in contact with TYR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASN 3.7 1.6 - - - +
16B LEU* 3.5 6.9 - - - +
17B ILE* 2.9 58.4 + - + +
53B PHE* 3.8 6.2 - - + -
71B HIS* 3.3 26.3 + + + -
72B PHE* 4.9 2.9 - - - -
138B GLY* 1.3 73.0 - - - -
140B VAL* 1.3 69.6 + - - +
141B GLN* 4.4 21.3 - - + -
148B ASN* 3.3 30.1 + - + -
149B TYR 3.4 11.9 - - - -
150B MET* 3.5 19.5 - - - -
151B PHE* 4.8 0.6 - - - -
234B SER 4.4 4.9 - - - -
235B GLU* 2.4 40.0 + - - -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 4.5 3.6 - - + -
3B ILE* 3.8 15.0 - - + -
14B LEU* 3.9 32.5 - - + -
15B ASN 3.8 2.2 - - - -
16B LEU* 3.4 27.6 - - + -
139B TYR* 1.3 74.4 - - - +
141B GLN* 1.3 62.8 + - - +
148B ASN* 3.2 7.1 - - - +
149B TYR* 2.6 60.4 + - + +
151B PHE* 3.6 24.9 - - + -
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLY 3.6 0.7 - - - +
14B LEU* 3.6 0.2 - - - -
15B ASN* 3.0 60.4 + - + +
17B ILE* 6.3 0.6 - - - +
139B TYR* 4.4 17.8 - - + -
140B VAL* 1.3 75.3 - - - +
142B ASP* 1.3 60.6 + - - +
143B THR* 3.4 10.3 + - - +
148B ASN* 3.5 16.3 + - - +
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Residues in contact with ASP 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 5.7 1.6 - - - +
14B LEU* 3.5 24.8 - - + +
140B VAL 3.8 1.8 - - - -
141B GLN* 1.3 72.7 - - - +
143B THR* 1.3 57.8 + - - +
144B ASN* 2.7 45.4 + - - +
145B ASN* 3.1 29.7 + - - +
146B GLN* 3.0 26.9 + - - -
147B ARG 2.8 21.1 + - - +
148B ASN* 5.0 0.3 - - - +
149B TYR* 4.0 15.3 + - + -
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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