Contacts of the strand formed by residues 33 - 39 (chain B) in PDB entry 3QAZ
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 CYS 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TRP* 4.0 15.3 - - + -
31B THR* 3.0 23.5 + - - +
32B SER* 1.3 73.7 + - - +
34B GLN* 1.3 64.5 + - - +
49B GLU* 3.6 3.8 - - - +
50B LEU* 2.7 53.1 + - + +
58B TRP* 5.7 6.7 - - + +
83B LEU 3.4 4.3 - - - +
84B CYS* 2.0 42.4 - - - -
90B TRP* 4.7 0.2 - - - -
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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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32B SER* 5.5 2.1 + - - +
33B CYS* 1.3 80.0 - - - +
35B VAL* 1.3 61.1 + - - +
36B HIS* 3.1 30.1 + - + +
47B THR* 4.6 9.5 + - - +
48B CYS 3.5 17.0 - - - +
49B GLU* 4.0 24.1 + - + +
50B LEU* 3.9 3.4 - - - -
82B VAL* 3.3 6.6 - - - +
83B LEU* 2.7 40.3 + - + +
90B TRP* 3.6 31.9 - - + -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 4.4 7.2 - - + -
20B CYS* 4.1 23.8 - - + -
34B GLN* 1.3 73.8 - - - +
36B HIS* 1.3 70.0 + - - +
46B GLN 3.8 0.7 - - - +
47B THR* 3.1 26.7 - - - -
48B CYS 3.4 6.6 + - - -
50B LEU* 3.7 23.3 - - + -
60B CYS* 4.6 9.9 - - + -
62B LEU* 3.9 24.6 - - + +
80B LEU* 4.8 3.8 - - + -
81B ARG 3.3 8.5 - - - +
82B VAL* 3.5 22.9 - - + -
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Residues in contact with HIS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 3.1 32.0 + - + +
35B VAL* 1.3 82.5 - - - +
37B ALA* 1.3 60.0 + - - +
38B TRP* 3.7 31.7 + + + +
46B GLN 3.7 3.1 - - - -
47B THR* 3.5 22.3 - - + +
79B THR 3.5 4.9 - - - +
80B LEU* 3.5 1.7 - - - +
81B ARG* 2.7 43.7 + - + +
83B LEU* 4.2 27.8 - - + +
90B TRP* 5.7 3.9 - + - -
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Residues in contact with ALA 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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18B ILE* 4.8 4.5 - - + -
35B VAL 4.2 0.2 + - - -
36B HIS* 1.3 71.1 - - - +
38B TRP* 1.3 62.4 + - - +
39B PRO* 3.4 4.5 - - - +
44B TRP* 4.7 2.4 - - + -
45B GLN* 3.3 7.3 - - - -
46B GLN* 2.9 37.2 + - + +
62B LEU* 3.6 20.2 - - + -
64B LEU* 5.1 5.2 - - + -
78B VAL* 3.9 7.6 - - + -
80B LEU* 3.4 25.8 - - + -
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Residues in contact with TRP 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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36B HIS* 3.7 39.1 + + + +
37B ALA* 1.3 74.4 - - - +
39B PRO* 1.3 70.6 - - - +
40B ASP* 3.4 1.9 + - - -
44B TRP 4.1 7.4 - - - -
45B GLN* 3.1 33.6 - - + +
47B THR* 6.2 1.1 - - + -
78B VAL* 3.8 1.7 - - - +
79B THR* 3.0 43.4 + - + +
81B ARG* 5.7 10.5 - - + +
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Residues in contact with PRO 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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37B ALA 3.4 8.3 - - - +
38B TRP* 1.3 87.0 - - + +
40B ASP* 1.3 61.8 - - - +
41B ARG 3.1 3.5 + - - +
42B ARG* 3.4 34.6 + - + +
44B TRP* 2.9 61.4 - - + +
72B LEU* 4.8 3.1 - - + -
76B ASP* 5.0 2.0 - - - +
77B ILE 3.9 6.1 - - - +
78B VAL* 4.1 14.1 - - + -
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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