Contacts of the strand formed by residues 53 - 61 (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 PHE 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B ILE* 3.3 44.0 - - + -
18B HIS* 3.5 24.5 - - - -
19B PRO* 3.6 22.0 - - + -
34B VAL 3.8 0.3 - - - +
35B TYR* 3.3 4.9 - - - -
36B ALA 2.8 38.4 + - - +
38B PRO* 4.4 10.5 - - + -
51B PRO* 5.5 0.7 - - + -
52B LEU* 1.3 78.0 - - - +
54B THR* 1.3 60.8 + - - +
55B LEU* 4.0 16.2 - - + -
69B ILE* 3.9 13.9 - - + -
70B GLU 3.7 14.6 - - - +
71B HIS* 4.9 8.7 - + + -
138B GLY* 4.1 8.7 - - - -
139B TYR* 3.8 20.0 - - + -
150B MET* 4.2 6.5 - - + -
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Residues in contact with THR 54 (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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352A GLN* 4.5 10.4 + - - -
353A LYS* 5.9 0.9 - - - -
33B VAL* 3.9 24.2 - - + -
34B VAL 3.7 2.5 - - - -
35B TYR* 3.8 21.2 - - + +
52B LEU* 4.1 7.6 + - - +
53B PHE* 1.3 76.5 + - - +
55B LEU* 1.3 63.0 + - - +
56B ARG* 5.4 7.6 - - + +
68B ARG 3.3 4.5 - - - +
70B GLU* 3.0 54.5 + - - +
73B GLN* 4.9 7.2 + - - +
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Residues in contact with LEU 55 (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* 4.6 3.8 - - + -
32B MET 3.7 0.9 - - - +
33B VAL* 3.3 4.0 - - - +
34B VAL* 2.7 52.5 + - + +
36B ALA* 4.3 13.7 - - + -
53B PHE* 4.0 22.7 - - + +
54B THR* 1.3 76.9 - - - +
56B ARG* 1.3 60.3 + - - +
57B PHE* 4.0 28.9 - - + -
67B VAL* 5.1 4.7 - - + -
68B ARG 3.4 4.9 - - - +
69B ILE* 4.1 23.8 - - + -
118B TRP* 4.3 24.0 - - + -
120B LEU* 4.8 11.2 - - + -
137B ASN* 5.2 3.8 - - - +
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Residues in contact with ARG 56 (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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28B GLN* 3.5 37.2 + - - +
31B GLU* 2.8 46.8 + - + +
32B MET 3.4 6.5 - - - +
33B VAL* 3.6 20.5 - - + +
54B THR* 4.0 7.5 + - + +
55B LEU* 1.3 75.1 - - - +
57B PHE* 1.3 69.4 + - - +
58B PHE* 3.8 12.4 - - + -
66B GLY 3.6 2.6 - - - +
67B VAL* 3.7 0.7 - - - -
68B ARG* 3.0 51.5 + - + +
70B GLU* 6.3 3.0 - - - -
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Residues in contact with PHE 57 (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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31B GLU* 3.5 6.1 - - - +
32B MET* 2.8 47.3 + - + +
34B VAL* 4.0 25.8 - - + -
55B LEU* 4.0 27.1 - - + -
56B ARG* 1.3 75.8 - - - +
58B PHE* 1.3 63.3 + - - +
65B VAL* 4.4 1.6 - - + -
66B GLY 3.2 5.6 - - - +
67B VAL* 3.8 33.2 - - + -
103B PHE* 3.8 26.0 - - + -
110B ALA* 3.7 31.4 - - + -
112B VAL* 3.9 22.7 - - + -
120B LEU* 4.6 11.4 - - + -
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Residues in contact with PHE 58 (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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31B GLU* 3.5 28.5 - - + +
56B ARG* 3.8 19.7 - - + -
57B PHE* 1.3 79.3 - - - +
59B SER* 1.3 64.3 + - - +
60B PRO* 4.6 7.9 - - + -
65B VAL 3.5 0.3 - - - -
66B GLY* 2.6 50.8 + - - -
67B VAL 4.1 1.6 - - - -
68B ARG* 4.3 13.5 - - + -
86B ILE* 5.6 10.1 - - + -
103B PHE* 3.4 18.6 - - - -
238B GLU* 3.7 20.2 - - - -
240B PHE* 3.7 32.8 - + - -
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Residues in contact with SER 59 (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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30B ASN* 5.1 7.6 + - - +
58B PHE* 1.3 82.2 - - - +
60B PRO* 1.3 62.9 - - - +
61B GLN 2.8 12.0 + - - -
64B ILE 2.6 19.5 + - - -
87B LEU 3.9 6.2 - - - +
90B VAL* 3.4 18.1 - - - +
92B VAL* 3.8 16.8 - - - +
103B PHE* 3.6 3.7 - - - -
105B SER* 2.7 31.8 + - - -
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Residues in contact with PRO 60 (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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58B PHE* 4.2 8.3 - - + +
59B SER* 1.3 84.5 - - - +
61B GLN* 1.3 79.6 + - - +
64B ILE* 3.5 27.6 - - + +
86B ILE* 4.0 20.6 - - + -
87B LEU* 3.0 27.1 + - - +
90B VAL* 3.7 2.5 - - - -
240B PHE* 4.0 15.3 - - + -
257B PHE* 3.6 39.9 - - + -
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Residues in contact with GLN 61 (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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59B SER* 2.8 18.8 + - - -
60B PRO* 1.3 91.9 + - - +
62B GLU* 1.3 68.1 - - - +
64B ILE* 2.9 28.1 + - + +
85B ASN* 2.8 32.7 + - - +
87B LEU* 3.1 30.6 - - - +
90B VAL* 3.9 7.2 - - - -
253B ARG* 5.6 0.9 - - + +
256B ARG* 3.5 36.8 - - + +
257B PHE* 3.8 19.3 - - + +
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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