Contacts of the strand formed by residues 53 - 58 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C ILE* 3.2 45.5 - - + -
18C HIS 3.4 8.1 - - - -
19C PRO* 3.4 48.5 - - + -
34C VAL 3.6 1.9 - - - +
35C TYR* 3.4 4.9 - - - -
36C ALA 3.0 37.7 + - - +
38C PRO* 4.4 8.7 - - + -
51C PRO* 5.6 0.7 - - + -
52C LEU* 1.3 74.4 - - - +
54C THR* 1.3 60.7 + - - +
55C LEU* 3.9 10.1 + - + +
69C ILE* 4.4 11.9 - - + -
70C GLU 3.8 13.9 - - - -
71C HIS* 4.4 10.3 - + + -
138C GLY* 4.1 3.4 - - - -
139C TYR* 3.8 20.0 - - + -
150C MET* 4.3 10.5 - - + -
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Residues in contact with THR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 3.9 25.1 - - + -
34C VAL 3.7 2.2 - - - -
35C TYR* 3.9 22.5 - - + +
52C LEU* 3.8 7.8 + - - +
53C PHE* 1.3 72.9 - - - +
55C LEU* 1.3 62.6 + - - +
56C ARG* 4.0 9.1 + - + +
68C ARG 3.3 3.6 - - - +
70C GLU* 3.0 48.4 + - + +
73C GLN* 4.0 18.6 + - - +
352E GLN* 4.4 4.2 + - - -
353E LYS* 6.0 0.7 - - - -
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PRO* 4.6 4.5 - - + -
32C MET 3.8 1.0 - - - +
33C VAL* 3.4 3.6 - - - +
34C VAL* 2.8 51.2 + - + +
36C ALA* 4.5 4.7 - - + -
53C PHE* 3.9 23.1 - - + +
54C THR* 1.3 78.1 - - - +
56C ARG* 1.3 60.3 + - - +
57C PHE* 4.1 28.1 - - + -
67C VAL* 5.2 1.1 - - + -
68C ARG 3.3 4.7 - - - +
69C ILE* 3.9 32.5 - - + -
112C VAL* 5.5 0.2 - - + -
118C TRP* 4.0 34.5 - - + -
120C LEU* 4.7 8.3 - - + -
137C ASN* 5.2 1.3 - - - +
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Residues in contact with ARG 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLN* 2.8 34.2 + - - +
31C GLU* 2.9 37.3 + - + +
32C MET 3.5 6.5 - - - +
33C VAL* 3.8 16.3 - - + +
54C THR* 4.0 7.8 + - + +
55C LEU* 1.3 75.4 - - - +
57C PHE* 1.3 70.3 + - - +
58C PHE* 3.8 11.7 - - + -
66C GLY 3.4 3.6 - - - +
67C VAL* 3.6 1.6 - - - -
68C ARG* 2.9 53.6 + - + +
70C GLU* 5.5 4.2 + - - +
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Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLU* 3.4 6.1 - - - +
32C MET* 2.8 49.7 + - + +
34C VAL* 4.1 15.9 - - + -
55C LEU* 4.1 28.7 - - + -
56C ARG* 1.3 73.5 - - - +
58C PHE* 1.3 60.8 + - - +
65C VAL* 4.3 1.3 - - + -
66C GLY 3.2 5.4 - - - +
67C VAL* 3.6 34.3 - - + -
103C PHE* 3.9 27.4 - - + -
110C ALA* 3.6 29.4 - - + -
112C VAL* 3.8 30.3 - - + -
120C LEU* 4.3 11.0 - - + -
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Residues in contact with PHE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLU* 3.4 33.0 - - + -
56C ARG* 3.8 18.4 - - + -
57C PHE* 1.3 76.3 - - - +
59C SER* 1.3 61.9 + - - +
60C PRO* 4.5 9.2 - - + -
65C VAL 3.6 0.2 - - - -
66C GLY* 2.7 48.2 + - - -
67C VAL 4.1 1.8 - - - -
68C ARG* 4.4 6.7 - - + -
86C ILE* 5.7 10.8 - - + -
103C PHE* 3.4 16.3 - - - -
238C GLU* 3.7 31.4 - - - -
240C PHE* 4.0 25.4 - + - -
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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