Contacts of the strand formed by residues 6 - 15 (chain B) in PDB entry 2CT8
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 LYS 6 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.3 39.8 + - - +
2B THR* 3.5 17.9 - - - +
4B MET 3.0 7.2 + - - +
5B LYS* 1.3 74.9 - - - +
7B PHE* 1.3 68.1 + - - +
8B TYR* 4.3 2.0 - - - +
43B TYR* 3.9 9.0 - - - -
44B ASP* 3.2 22.2 - - + +
247B ILE* 3.2 17.3 - - + +
248B TYR* 3.0 45.5 - - + -
250B PRO* 3.2 13.5 + - - -
252B ASP* 2.8 31.3 + - - +
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Residues in contact with PHE 7 (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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6B LYS* 1.3 77.6 - - - +
8B TYR* 1.3 58.8 + - - +
9B VAL* 3.8 27.4 - - + -
34B ILE* 4.2 18.4 - - + -
35B ALA* 5.0 0.2 - - - -
38B TYR* 3.4 57.0 - + + -
43B TYR* 4.1 14.8 - + + -
44B ASP 2.9 7.5 + - - +
45B VAL* 3.3 15.2 - - + +
46B PHE* 3.1 24.4 + - - +
248B TYR* 5.2 0.2 - - - -
252B ASP* 3.6 29.6 - - + -
253B LEU* 4.3 20.0 - - + -
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Residues in contact with TYR 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 4.3 2.4 - - + +
7B PHE* 1.3 75.1 - - - +
9B VAL* 1.3 61.9 + - - +
10B THR* 3.3 22.2 - - + +
46B PHE* 3.2 39.5 - + + +
48B LEU* 3.8 11.4 - - + +
237B TYR* 2.4 35.2 + - - -
240B ALA* 5.2 0.3 - - - +
241B LEU* 3.5 26.7 - - + +
248B TYR* 3.4 37.5 - - + +
249B TRP* 3.4 12.1 - + - -
251B ALA* 3.6 17.1 - - + +
252B ASP* 2.9 38.6 + - - +
253B LEU 3.3 5.9 + - - +
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 3.8 24.9 - - + -
8B TYR* 1.3 74.0 - - - +
10B THR* 1.3 77.4 + - - +
31B ALA* 4.2 4.7 - - + +
34B ILE* 3.9 19.3 - - + -
35B ALA* 4.3 14.6 - - + -
45B VAL* 5.0 0.7 - - + -
46B PHE 3.2 10.4 + - - +
47B PHE* 4.1 18.6 - - + -
48B LEU 3.1 22.2 + - - -
253B LEU* 3.4 17.7 - - + +
255B LEU* 4.0 13.5 - - + -
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Residues in contact with THR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B TYR* 3.3 37.7 - - + +
9B VAL* 1.3 85.2 - - - +
11B THR* 1.3 64.3 + - - +
31B ALA* 4.9 0.2 - - - -
48B LEU* 3.5 12.8 - - + -
237B TYR* 3.3 26.4 - - + -
251B ALA* 4.8 1.1 - - + -
253B LEU 3.0 5.5 + - - +
254B HIS* 2.8 33.7 + - + +
255B LEU* 3.2 26.3 + - - +
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Residues in contact with THR 11 (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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10B THR* 1.3 74.5 - - - +
12B PRO* 1.3 86.8 + - - +
13B ILE* 4.8 2.1 - - - +
14B TYR* 3.6 9.6 + - - -
27B THR* 4.5 2.9 - - - +
28B THR* 4.0 15.7 - - - +
31B ALA* 3.5 31.0 - - + -
47B PHE* 3.7 8.3 - - + -
48B LEU* 3.1 14.0 + - - +
49B THR* 3.1 23.9 + - - +
236B ASN* 5.2 0.2 - - - +
237B TYR* 3.5 17.5 - - - -
255B LEU 3.8 3.1 - - - -
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Residues in contact with PRO 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B THR* 1.3 103.6 + - - +
13B ILE* 1.3 61.9 + - - +
14B TYR* 3.5 21.9 + - + +
27B THR* 3.5 13.7 - - + -
50B GLY 4.3 1.2 + - - +
237B TYR* 3.8 11.0 - - - +
255B LEU 3.1 19.1 - - - +
256B VAL* 3.8 10.3 - - + -
260B ILE* 3.9 12.6 - - + -
1501B MSP 3.4 41.1 - - + +
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Residues in contact with ILE 13 (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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11B THR 3.7 2.2 + - - +
12B PRO* 1.3 73.4 - - - +
14B TYR* 1.3 59.8 + - - +
48B LEU* 5.6 0.2 - - + -
49B THR 4.8 0.4 - - - -
50B GLY* 3.6 20.6 - - - +
51B THR 3.7 2.9 - - - +
52B ASP* 3.5 20.6 - - + +
95B ILE* 3.8 11.7 - - + -
97B THR* 4.0 11.4 - - + -
233B ALA* 3.3 43.3 - - + +
236B ASN* 3.3 31.4 - - + +
1501B MSP 2.9 45.1 + - + +
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Residues in contact with TYR 14 (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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11B THR* 3.6 8.8 - - - -
12B PRO* 3.7 21.3 - - + -
13B ILE* 1.3 72.3 - - - +
15B TYR* 1.3 64.5 + - - +
24B HIS* 3.1 23.2 + + + -
27B THR* 3.3 16.1 - - - -
28B THR* 2.9 28.4 + - - -
49B THR* 4.0 7.6 - - - -
50B GLY 3.2 17.0 + - - +
51B THR* 3.3 9.9 - - - +
52B ASP 2.9 21.1 + - - -
80B PHE* 3.6 37.5 - + + -
84B TRP* 3.6 12.6 - + - -
1501B MSP 3.0 49.6 - - - +
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Residues in contact with TYR 15 (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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14B TYR* 1.3 74.4 - - - +
16B VAL* 1.3 60.4 + - - +
17B ASN* 3.5 25.7 + - + +
18B ASP 4.2 2.1 - - - +
24B HIS* 5.2 1.9 + - - -
52B ASP* 3.7 24.3 + - + -
54B HIS 5.1 10.1 - - - -
57B LYS* 5.5 17.3 + - + -
58B ILE* 5.4 5.4 - - + -
80B PHE* 3.5 16.5 - - - -
229B VAL* 4.7 12.0 - - + +
230B TRP* 3.3 31.0 + + - -
1501B MSP 3.0 66.9 + - - +
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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