Contacts of the strand formed by residues 64 - 70 (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 ILE 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B SER* 2.6 33.6 + - - -
60B PRO* 3.6 21.5 - - + -
61B GLN* 2.9 23.8 + - + +
63B GLY* 1.3 84.5 - - - +
65B VAL* 1.3 65.2 + - - +
105B SER* 4.0 1.0 + - - -
240B PHE* 3.9 25.1 - - + -
241B VAL 3.5 5.4 - - - +
242B ILE* 3.7 28.0 - - + -
253B ARG* 4.2 12.3 - - + +
257B PHE* 3.7 36.8 - - + -
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 4.4 2.0 - - + -
58B PHE 3.5 2.2 - - - -
64B ILE* 1.3 75.4 - - - +
66B GLY* 1.3 70.1 + - - +
67B VAL* 3.8 10.3 + - + +
103B PHE* 4.0 20.6 - - + -
105B SER* 4.2 11.2 - - - -
108B LEU* 3.6 42.8 - - + +
109B SER* 4.7 3.4 - - - -
110B ALA* 4.0 24.2 - - + +
122B PHE* 4.5 6.1 - - + -
239B TYR 3.9 0.3 - - - +
240B PHE* 3.4 3.4 - - - -
241B VAL* 3.0 30.7 + - + +
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 3.2 7.6 - - - -
58B PHE* 2.6 47.9 + - - -
60B PRO* 4.4 0.6 - - - +
64B ILE 4.0 1.0 + - - -
65B VAL* 1.3 75.0 - - - +
67B VAL* 1.3 61.6 + - - +
239B TYR 3.7 0.4 - - - -
240B PHE* 3.4 30.2 - - - -
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 5.1 7.6 - - + -
56B ARG 3.7 2.7 - - - +
57B PHE* 3.8 29.4 - - + -
58B PHE* 4.1 1.5 - - - -
65B VAL* 4.2 7.2 - - + +
66B GLY* 1.3 77.3 - - - +
68B ARG* 1.3 65.4 + - - +
69B ILE* 4.9 4.0 - - + +
120B LEU* 4.8 5.4 - - + -
122B PHE* 3.7 32.8 - - + -
237B LEU 3.7 1.2 - - - +
238B GLU* 3.2 4.8 - - - +
239B TYR* 2.9 66.7 + - + +
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Residues in contact with ARG 68 (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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54B THR 3.3 6.2 - - - +
55B LEU* 4.4 0.7 - - - -
56B ARG* 3.0 53.0 + - + +
58B PHE* 4.3 6.7 - - + -
67B VAL* 1.3 75.5 - - - +
69B ILE* 1.3 60.6 + - - +
70B GLU* 2.6 36.8 + - + +
77B ASN* 5.1 4.8 - - - +
236B TYR* 3.6 44.4 - - + +
237B LEU 3.3 8.3 - - - +
238B GLU* 2.9 35.4 + - + +
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Residues in contact with ILE 69 (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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19B PRO* 4.4 18.2 - - + -
53B PHE* 3.9 23.6 - - + -
54B THR 3.6 2.9 - - - -
55B LEU* 4.1 24.0 - - + +
67B VAL* 4.1 3.5 - - + -
68B ARG* 1.3 73.6 - - - +
70B GLU* 1.3 60.4 + - - +
137B ASN* 4.6 10.8 - - + +
138B GLY 4.5 11.4 - - - +
150B MET* 3.4 22.0 - - + +
151B PHE 5.5 1.6 - - - +
152B GLU* 6.1 1.1 - - + +
236B TYR* 3.3 2.3 - - - +
237B LEU* 2.8 68.6 + - + +
239B TYR* 5.2 8.1 - - + -
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Residues in contact with GLU 70 (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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52B LEU 4.4 0.2 - - - +
53B PHE* 3.7 13.9 - - - -
54B THR* 3.0 45.9 + - - +
56B ARG* 6.3 2.9 - - - -
68B ARG* 2.6 46.4 + - + +
69B ILE* 1.3 77.5 - - - +
71B HIS* 1.3 67.0 + - - +
72B PHE 5.2 1.6 - - - +
73B GLN* 2.7 40.4 + - + +
150B MET* 4.8 1.3 - - - -
235B GLU 3.9 3.6 - - - +
236B TYR* 4.0 10.3 - - + +
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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