Contacts of the strand formed by residues 31 - 37 (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 GLU 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C GLN* 3.6 1.9 - - - -
28C GLN* 2.8 40.4 + - - +
29C ASP 3.4 0.6 - - - -
30C ASN* 1.3 97.6 - - - +
32C MET* 1.3 60.4 + - - +
33C VAL* 4.0 0.4 + - - -
56C ARG* 2.9 46.2 + - + +
57C PHE 3.4 6.3 - - - +
58C PHE* 3.4 30.0 - - + +
94C ILE* 3.6 4.8 - - - +
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Residues in contact with MET 32 (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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25C VAL* 4.3 12.6 - - + -
26C GLU 3.8 7.2 - - - +
27C GLN* 4.7 0.4 - - - +
31C GLU* 1.3 72.5 - - - +
33C VAL* 1.3 62.8 + - - +
34C VAL* 4.6 8.7 - - + -
56C ARG* 3.5 2.1 - - - -
57C PHE* 2.8 47.6 + - + +
94C ILE* 3.1 37.7 - - + +
95C GLU 3.9 4.7 - - - +
96C ASN* 5.4 0.2 - - - -
101C ALA* 3.9 17.3 - - + +
102C GLU 2.9 53.8 - - - +
103C PHE* 3.5 18.1 - - + +
110C ALA 5.4 0.7 - - - +
112C VAL* 6.0 0.7 - - - -
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Residues in contact with VAL 33 (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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24C GLU 4.2 0.2 - - - +
25C VAL* 3.3 3.6 - - - +
26C GLU* 2.7 49.1 + - + +
28C GLN* 3.0 36.3 - - + +
31C GLU 4.6 1.6 - - - +
32C MET* 1.3 76.6 - - - +
34C VAL* 1.3 64.3 + - - +
35C TYR* 3.8 32.4 - - + +
54C THR* 3.9 20.4 - - + -
55C LEU 3.4 4.9 - - - +
56C ARG* 3.8 22.7 - - + +
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Residues in contact with VAL 34 (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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22C VAL* 4.1 24.2 - - + -
24C GLU 3.6 7.0 - - - +
25C VAL* 4.2 16.4 - - + -
32C MET* 4.6 4.0 - - + -
33C VAL* 1.3 79.2 - - - +
35C TYR* 1.3 73.6 + - - +
36C ALA* 4.6 0.4 - - + +
53C PHE 3.6 1.9 - - - +
54C THR* 3.7 0.9 - - - -
55C LEU* 2.8 49.3 + - + +
57C PHE* 4.1 21.3 - - + -
101C ALA* 4.6 6.7 - - + -
112C VAL* 4.4 12.3 - - + -
118C TRP* 4.5 13.5 - - + -
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Residues in contact with TYR 35 (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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22C VAL* 3.7 2.9 - - - -
23C PHE* 2.8 33.0 + - + -
24C GLU* 2.9 46.9 + - + +
26C GLU* 3.5 23.4 + - + -
28C GLN* 5.2 3.1 + - - -
33C VAL* 3.8 21.2 - - + +
34C VAL* 1.3 74.2 - - - +
36C ALA* 1.3 59.1 + - - +
52C LEU* 3.6 27.1 - - + -
53C PHE 3.4 2.9 - - - -
54C THR* 3.9 26.1 - - + +
353E LYS* 3.8 45.1 + - + -
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Residues in contact with ALA 36 (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* 3.5 20.0 - - + -
21C GLN 3.0 12.8 - - - +
23C PHE 4.2 0.4 - - - +
34C VAL* 3.9 1.3 + - + -
35C TYR* 1.3 74.9 - - - +
37C ALA* 1.3 59.7 + - - +
38C PRO* 4.2 0.7 - - - +
52C LEU* 3.1 9.0 - - - +
53C PHE* 3.0 35.9 + - - +
55C LEU* 4.5 3.8 - - + -
118C TRP* 3.5 29.8 - - + -
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Residues in contact with ALA 37 (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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18C HIS 4.2 0.7 - - - -
19C PRO* 4.3 0.7 - - - -
20C LEU 2.7 27.9 + - - -
21C GLN 2.7 19.3 + - - +
23C PHE* 4.8 1.5 - - + +
36C ALA* 1.3 73.4 - - - +
38C PRO* 1.3 60.9 - - + +
39C ARG 3.1 24.4 + - - +
41C VAL* 3.4 34.1 - - + -
50C THR* 5.2 1.1 - - + +
51C PRO 4.9 0.4 - - - +
52C LEU* 4.1 8.7 - - + -
313E PHE* 5.6 0.9 - - + -
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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