Contacts of the strand formed by residues 36 - 46 (chain B) in PDB entry 3RCZ
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 LEU 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B ARG* 3.4 37.5 - - + +
28B PRO* 4.3 18.6 - - + +
29B CYS 3.6 6.7 - - - +
30B LYS* 5.7 0.4 - - - -
31B SER* 3.6 10.5 + - - -
35B GLY* 1.3 80.9 - - - +
37B ASP* 1.3 59.0 + - - +
38B LEU* 3.6 26.2 + - + +
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Residues in contact with ASP 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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28B PRO* 3.4 7.7 - - - +
29B CYS* 2.8 24.3 + - + +
30B LYS 4.2 2.2 - - - +
31B SER* 3.6 20.7 - - - +
36B LEU* 1.3 69.8 - - - +
38B LEU* 1.3 62.8 + - - +
39B MET* 3.1 23.4 + - - +
40B ASN* 2.9 45.7 + - - +
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Residues in contact with LEU 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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6B LYS* 3.7 30.3 - - + +
9B LEU* 3.4 40.4 - - + +
10B GLN* 3.5 34.5 - - + +
13B ARG* 4.9 3.8 - - + -
28B PRO* 3.8 23.3 - - + -
36B LEU* 3.6 23.6 + - + +
37B ASP* 1.3 72.6 + - - +
39B MET* 1.3 62.2 + - + +
40B ASN 3.3 0.7 - - - -
41B TRP* 2.7 26.2 + - + +
64B PHE* 3.9 0.7 - - - -
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Residues in contact with MET 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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5B CYS* 3.5 25.4 - - - -
6B LYS* 5.6 2.9 - - - -
9B LEU* 3.8 9.0 - - - -
37B ASP* 3.1 13.6 - - - +
38B LEU* 1.3 82.2 - - + +
40B ASN* 1.3 68.8 + - - +
63B ALA* 3.5 0.2 - - - -
64B PHE* 2.7 66.6 + - + +
65B PRO 3.2 24.5 - - - +
66B GLU* 3.9 7.4 - - + +
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Residues in contact with ASN 40 (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 CYS* 2.7 44.0 + - - -
37B ASP* 2.9 31.3 + - - +
38B LEU 3.3 0.6 - - - -
39B MET* 1.3 91.6 - - - +
41B TRP* 1.3 57.1 + - - +
62B MET 3.4 3.9 - - - +
63B ALA* 3.7 19.2 - - - +
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Residues in contact with TRP 41 (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 LEU* 3.9 20.9 - - + +
12B GLU 4.4 0.4 - - - -
13B ARG* 3.7 32.8 - - + -
16B TRP* 5.2 6.1 - + + -
26B ALA* 3.9 25.6 - - + -
27B LYS 3.2 21.8 - - - +
28B PRO* 3.7 22.4 - - + +
29B CYS* 4.4 1.1 - - - -
38B LEU* 2.7 33.0 + - + -
40B ASN* 1.3 77.9 - - - +
42B LYS* 1.3 64.6 + - - +
43B VAL* 4.3 10.8 - - + -
61B THR* 3.4 8.5 - - - +
62B MET* 3.0 36.5 + - + +
64B PHE* 3.4 17.5 - + - -
109B ILE* 3.6 35.4 - - + -
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Residues in contact with LYS 42 (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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25B TYR* 3.8 7.6 - - + +
26B ALA* 3.5 1.7 - - - -
27B LYS* 2.8 57.7 + - + +
29B CYS* 3.9 26.5 - - - +
41B TRP* 1.3 76.3 - - - +
43B VAL* 1.3 61.2 + - - +
60B LEU 3.7 6.1 - - - +
61B THR* 4.9 11.7 - - + -
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Residues in contact with VAL 43 (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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25B TYR* 3.1 22.6 + - - +
26B ALA* 3.8 17.5 - - + -
41B TRP* 4.3 6.1 - - + -
42B LYS* 1.3 80.8 - - - +
44B GLY* 1.3 62.7 + - - +
59B LYS* 3.4 4.9 - - - +
60B LEU* 2.9 57.0 + - + +
62B MET* 3.9 31.9 - - + -
113B LEU* 3.8 25.6 - - + -
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Residues in contact with GLY 44 (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* 3.3 10.6 - - - +
25B TYR* 2.9 51.8 + - - +
43B VAL* 1.3 75.6 - - - +
45B ILE* 1.3 65.7 + - - +
57B LEU* 3.8 9.9 - - - -
58B TYR 3.4 7.4 - - - -
113B LEU* 5.3 0.2 - - - +
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Residues in contact with ILE 45 (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* 3.8 14.6 - - + -
43B VAL* 4.6 0.2 - - + -
44B GLY* 1.3 77.5 - - - +
46B PRO* 1.3 66.2 - - - +
57B LEU* 3.7 2.4 - - - +
58B TYR* 2.7 48.2 + - + +
60B LEU* 3.3 27.1 - - + -
77B PHE* 4.9 0.9 - - + -
113B LEU* 3.7 24.5 - - + +
116B ILE* 3.5 31.2 - - + -
117B GLN* 3.7 32.1 - - + -
120B LEU* 4.3 9.0 - - + -
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Residues in contact with PRO 46 (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 PHE 4.1 4.7 - - - +
23B GLY* 3.6 27.1 - - - +
24B PHE* 3.4 40.8 - - + -
45B ILE* 1.3 86.2 - - - +
47B GLY* 1.3 65.5 + - - +
56B GLY 3.4 9.0 - - - +
57B LEU* 4.0 5.8 - - + -
58B TYR* 4.5 0.7 - - - -
117B GLN* 2.9 33.6 - - - +
120B LEU* 4.5 0.2 - - - +
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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