Contacts of the strand formed by residues 19 - 27 (chain B) in PDB entry 3CP7
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 GLY 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B SER* 3.3 3.1 - - - -
16B THR 2.9 32.5 + - - +
17B ASN 3.5 1.0 - - - -
18B GLN* 1.3 79.8 - - - +
20B ASP* 1.3 66.6 + - - +
21B PHE* 3.4 12.2 - - - -
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B PHE 3.6 4.5 - - - +
15B SER* 2.6 28.9 + - - +
19B GLY* 1.3 74.5 - - - -
21B PHE* 1.3 70.7 + - - +
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Residues in contact with PHE 21 (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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13B PHE* 3.5 2.4 - - - +
14B PHE* 2.8 63.7 + + + +
16B THR* 3.5 21.1 - - + -
18B GLN* 3.8 25.1 - - + -
19B GLY* 3.4 26.7 - - - -
20B ASP* 1.3 80.5 - - - +
22B VAL* 1.3 71.4 + - - +
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Residues in contact with VAL 22 (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 LYS* 3.9 22.0 - - - +
12B VAL 3.2 12.8 - - - +
13B PHE* 3.8 21.3 - - + -
14B PHE* 4.0 3.4 - - - -
21B PHE* 1.3 84.4 - - - +
23B CYS* 1.3 73.4 + - - +
132B ALA* 3.8 28.5 - - + -
167B GLY* 3.8 15.3 - - - +
219B FMT 3.8 6.8 - - - -
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Residues in contact with CYS 23 (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 LYS* 3.8 8.8 - - - +
12B VAL* 2.9 39.0 + - + +
14B PHE* 3.8 9.2 - - + -
22B VAL* 1.3 81.1 - - - +
24B SER* 1.3 64.2 + - - +
41B HIS* 4.7 0.2 - - - -
42B CYS* 2.1 54.5 - - + -
130B TYR* 4.7 0.9 - - - +
167B GLY 3.1 16.9 - - - +
169B SER 3.7 3.1 - - - -
219B FMT 3.7 17.3 - - - -
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Residues in contact with SER 24 (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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9B ILE* 5.8 0.9 - - - -
10B GLY 3.4 13.2 - - - -
12B VAL* 3.6 5.5 - - - +
23B CYS* 1.3 73.2 + - - +
25B ALA* 1.3 62.5 + - - +
38B THR* 2.9 22.2 + - - -
129B GLY* 3.6 4.0 - - - -
130B TYR* 2.9 27.5 + - - +
167B GLY 2.9 16.6 + - - -
168B SER* 3.6 2.0 - - - -
169B SER 2.8 6.9 + - - -
170B GLY* 3.2 9.5 - - - -
171B GLY* 3.6 22.7 - - - -
172B PRO* 5.5 0.2 - - - -
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Residues in contact with ALA 25 (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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9B ILE* 3.7 7.3 - - - +
10B GLY 3.0 28.2 + - - +
12B VAL* 3.6 17.5 - - + -
24B SER* 1.3 78.0 - - - +
26B ASN* 1.3 64.8 + - - +
36B VAL* 4.1 11.0 - - + -
37B ALA 3.3 16.4 - - - +
38B THR* 3.9 7.2 - - - -
57B PHE* 3.7 16.2 - - + -
170B GLY 3.6 5.6 - - - -
172B PRO* 4.2 2.0 - - - +
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Residues in contact with ASN 26 (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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8B HIS* 2.8 37.7 + - - +
9B ILE* 3.3 6.2 + - - +
25B ALA* 1.3 79.5 - - - +
27B ILE* 1.3 67.2 + - - +
28B VAL* 3.3 2.6 + - - +
36B VAL* 3.1 4.8 - - - -
37B ALA* 2.8 33.9 + - - +
57B PHE* 4.5 0.2 - - - -
113B SER* 3.0 29.5 + - - -
172B PRO* 3.8 19.3 - - + -
174B PHE* 3.6 6.4 - - - -
183B GLN* 2.9 29.0 + - - +
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Residues in contact with ILE 27 (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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8B HIS* 2.9 34.6 + - + +
26B ASN* 1.3 77.4 + - - +
28B VAL* 1.3 62.6 + - - +
35B THR 3.6 13.0 - - - +
36B VAL* 3.9 5.6 - - + -
57B PHE* 3.7 18.8 - - + -
59B PRO* 4.6 0.2 - - + -
105B VAL* 3.9 24.5 - - + +
106B GLN* 3.6 30.3 - - + -
109B VAL* 3.8 36.1 - - + -
111B THR 4.2 2.5 - - - +
112B ALA* 3.6 8.8 - - + -
113B SER* 2.9 20.8 + - - -
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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