Contacts of the strand formed by residues 23 - 32 (chain B) in PDB entry 4CBO
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 ALA 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B GLN* 3.2 5.4 - - - +
20B LEU* 2.7 38.5 + - - +
21B ASN 3.4 3.2 + - - +
22B GLY* 1.3 77.3 - - - +
24B HIS* 1.3 67.0 + - - +
137B ARG* 5.9 4.9 - - - +
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Residues in contact with HIS 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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17B SER* 2.8 30.2 + - - +
18B VAL 3.8 1.6 - - - -
19B GLN* 4.2 5.7 - - - +
23B ALA* 1.3 78.5 - - - +
25B LEU* 1.3 61.1 + - - +
26B CYS 3.2 31.5 + - - -
27B GLY* 3.9 1.3 - - - -
60B LEU* 3.7 23.9 - - + +
128B TRP* 3.9 45.1 - + + +
181B GLY* 2.9 27.9 + - - -
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Residues in contact with LEU 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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18B VAL* 2.7 26.9 + - + +
20B LEU* 3.9 47.8 - - + +
23B ALA 3.4 0.2 + - - -
24B HIS* 1.3 79.1 - - - +
26B CYS* 1.3 71.6 + - - +
42B CYS* 3.5 34.1 - - + +
43B LEU* 5.4 1.1 - - - -
44B GLU* 4.8 10.3 - - - +
45B ASP* 4.8 9.6 - - - +
51B VAL* 6.1 1.8 - - + -
181B GLY* 4.1 12.8 - - - -
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Residues in contact with CYS 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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18B VAL* 2.7 38.6 + - + -
24B HIS* 3.2 14.9 + - - -
25B LEU* 1.3 93.2 - - + +
27B GLY* 1.3 64.8 + - - +
38B SER* 4.2 0.7 - - - +
41B HIS* 4.3 2.0 - - - -
42B CYS* 2.0 53.6 - - + -
44B GLU* 5.2 1.3 - - - -
181B GLY 3.9 3.1 - - - -
183B SER* 3.1 17.3 - - - +
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Residues in contact with GLY 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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15B MET* 3.6 19.1 - - - -
16B ALA 3.6 2.2 - - - -
18B VAL* 3.5 3.1 - - - +
24B HIS* 4.4 3.4 - - - -
26B CYS* 1.3 76.2 - - - +
28B GLY* 1.3 53.7 + - - -
38B SER* 2.7 28.2 + - - -
128B TRP 6.2 0.2 - - - -
181B GLY 3.8 7.0 + - - -
182B ASP* 4.4 2.2 - - - -
183B SER 2.5 13.1 + - - +
184B GLY 3.1 10.3 - - - +
185B GLY* 3.8 6.5 - - - -
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Residues in contact with GLY 28 (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 3.8 0.3 - - - +
15B MET* 3.6 11.0 - - - +
16B ALA* 2.9 34.1 + - - +
18B VAL* 4.6 1.3 - - - -
27B GLY* 1.3 74.3 - - - -
29B VAL* 1.3 61.1 + - - +
36B VAL* 4.1 9.0 - - - -
37B LEU 3.1 13.9 - - - -
38B SER* 4.2 1.1 - - - -
184B GLY 3.2 7.2 + - - -
185B GLY* 3.8 0.4 - - - -
186B PRO* 4.0 4.0 - - - +
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Residues in contact with VAL 29 (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* 3.5 26.5 - - + -
28B GLY* 1.3 75.0 - - - +
30B LEU* 1.3 72.4 + - - +
31B VAL* 3.1 7.5 + - + -
36B VAL* 3.3 6.1 - - - +
37B LEU* 2.8 63.2 + - + +
108B LEU* 4.4 5.6 - - + -
184B GLY 5.4 0.9 - - - +
186B PRO* 4.0 10.8 - - + -
193B LEU* 3.5 38.6 - - + -
196B VAL* 5.2 3.4 - - + -
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Residues in contact with LEU 30 (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 PRO 4.9 0.9 - - - +
14B TYR* 2.8 21.7 + - - +
16B ALA* 4.8 0.8 - - - +
29B VAL* 1.3 72.0 - - - +
31B VAL* 1.3 59.3 + - - +
32B ALA 2.9 26.5 - - - +
33B GLU 4.2 7.4 - - - +
35B TRP 3.7 7.9 - - - +
36B VAL* 3.7 18.2 - - + +
55B LEU* 4.3 20.2 - - + -
95B LEU* 4.3 1.8 - - + -
99B ALA* 4.6 2.0 - - + -
101B LEU* 4.3 6.5 - - + -
105B VAL* 4.0 24.2 - - + -
106B ARG 3.7 6.7 - - - +
107B PRO* 3.1 29.2 - - + +
108B LEU* 2.9 26.0 + - - -
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Residues in contact with VAL 31 (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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29B VAL* 3.6 31.0 - - + +
30B LEU* 1.3 75.3 - - - +
32B ALA* 1.3 62.7 + - + +
35B TRP* 3.0 17.2 + - + +
37B LEU* 4.1 17.3 - - + +
92B LEU* 4.5 10.8 - - + -
107B PRO* 3.9 8.1 - - - +
108B LEU 3.9 13.9 - - - +
110B TRP* 3.6 37.8 + - + +
193B LEU* 4.0 9.4 - - + -
223B ILE* 5.4 4.5 - - + -
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Residues in contact with ALA 32 (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 LEU* 2.9 24.8 - - - +
31B VAL* 1.3 81.0 - - + +
33B GLU* 1.3 80.7 + - - +
34B GLN 2.9 3.2 + - - +
35B TRP* 3.0 34.5 + - + +
107B PRO* 4.3 6.7 - - - -
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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