Contacts of the strand formed by residues 33 - 39 (chain B) in PDB entry 4K71
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 GLN 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B TRP* 3.3 4.9 - - - -
30B LEU* 2.9 34.8 + - + +
31B GLY 3.3 0.6 - - - -
32B PRO* 1.3 77.1 - - - +
34B GLN* 1.3 61.9 + - - +
35B TYR 3.4 0.7 + - - -
50B ALA* 5.6 1.7 - - - +
51B TRP* 3.1 31.9 + - - +
173B ASN* 2.7 33.8 + - - +
174B LEU* 3.6 14.4 - - + +
176B TRP* 4.5 8.3 - - + -
204B TYR* 2.9 40.6 + - + +
232B GLY* 5.7 4.3 - - - +
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Residues in contact with GLN 34 (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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27B SER* 3.5 14.2 - - - -
28B GLY 3.4 13.5 - - - +
29B TRP* 3.4 34.8 - - + -
33B GLN* 1.3 72.0 - - - +
35B TYR* 1.3 59.4 + - - +
36B LEU 3.2 18.9 + - - +
48B CYS* 3.7 31.3 - - + +
49B GLY* 5.7 0.2 - - - -
51B TRP* 3.9 9.3 + - - -
52C SER* 5.6 2.9 - - - -
53C ASP* 2.7 38.3 + - - +
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Residues in contact with TYR 35 (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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7B LEU* 3.1 31.6 - - + +
9B TYR* 3.1 19.9 + - - -
28B GLY* 2.9 37.6 + - - -
29B TRP 3.7 1.8 - - - -
30B LEU* 3.8 30.1 - - + -
33B GLN 3.4 2.9 + - - +
34B GLN* 1.3 73.7 - - - +
36B LEU* 1.3 71.2 + - + +
47B PRO* 3.2 8.5 - - - +
48B CYS* 2.9 23.9 + - - -
51B TRP* 3.7 24.1 - + + +
60B TYR* 3.6 11.7 + - - -
61B TRP* 3.6 13.8 - + - -
64B GLU* 2.7 28.9 + - - -
166B HIS* 3.7 15.0 - + - -
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Residues in contact with LEU 36 (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 TYR* 4.1 5.8 - - + -
26B VAL* 4.0 12.1 - - + +
27B SER* 3.3 0.2 - - - -
28B GLY* 2.7 40.3 + - - +
34B GLN* 3.2 10.6 + - - +
35B TYR* 1.3 99.8 - - + +
37B SER* 1.3 76.0 + - - +
45B ALA* 4.2 2.7 - - + -
46B GLU 3.3 5.4 - - - -
48B CYS* 3.8 3.8 - - - -
61B TRP* 3.7 16.8 - - + -
64B GLU* 3.4 42.0 - - + +
68B LEU* 3.9 22.0 - - + -
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Residues in contact with SER 37 (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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26B VAL 3.5 6.1 - - - -
34B GLN* 3.7 3.4 - - - -
36B LEU* 1.3 76.3 - - - +
38B TYR* 1.3 65.7 + - - +
39B ASN* 5.5 3.1 + - - -
44B GLU 3.5 2.6 - - - +
45B ALA* 3.5 2.1 - - - -
46B GLU* 3.0 36.8 + - - +
48B CYS* 3.7 11.0 - - - -
53C ASP* 2.6 32.2 + - - -
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Residues in contact with TYR 38 (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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24B PHE* 3.7 27.4 - + - -
25B TRP* 3.1 5.4 - - - +
26B VAL* 2.7 42.2 + - + +
37B SER* 1.3 78.3 + - - +
39B ASN* 1.3 76.5 + - - +
43B GLY* 3.7 25.3 - - - -
44B GLU 3.7 7.4 - - - -
45B ALA* 3.7 21.8 - - + -
65B THR* 4.3 10.1 - - - -
68B LEU* 3.7 36.8 - - + -
69B ARG* 3.3 22.6 - - + +
72B GLU* 2.6 30.2 + - - -
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Residues in contact with ASN 39 (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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22B PRO* 3.7 24.7 - - + +
24B PHE 3.4 7.4 - - - +
25B TRP* 3.8 7.0 - - + -
37B SER* 5.5 3.2 + - - -
38B TYR* 1.3 84.3 - - - +
40B SER* 1.3 54.7 + - - +
41B LEU* 2.9 12.2 + - - +
42B ARG* 2.9 34.1 + - - +
43B GLY* 2.8 34.3 + - - +
44B GLU 4.6 2.2 + - - -
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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