Contacts of the strand formed by residues 29 - 34 (chain A) in PDB entry 6B0B
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 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.4 26.5 - - + -
8A THR* 4.7 12.1 - - + +
9A PHE* 6.4 0.4 - - - -
12A GLN* 3.8 35.7 - - + +
13A PHE* 5.1 6.5 - - + -
27A LYS* 5.3 5.2 - - + +
28A ALA* 1.3 84.4 - - - +
30A LEU* 1.3 64.6 + - - +
31A CYS* 5.3 2.2 - - - -
46A TYR* 5.2 7.2 - - + -
47A PHE 3.6 3.6 - - - +
48A GLU* 3.6 26.5 - - + +
55A ALA* 4.8 2.2 - - - -
80A LEU* 3.4 6.3 - - - +
81A THR* 2.7 42.3 + - + -
82A TRP 4.3 2.3 + - - +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 1.3 75.1 - - - +
31A CYS* 1.3 70.2 + - - +
32A TYR* 3.8 21.8 - - + +
46A TYR* 3.2 5.4 - - - +
47A PHE* 2.8 35.7 + - + +
55A ALA* 3.7 29.4 - - + +
56A GLU* 4.0 28.0 - - + +
59A PHE* 3.7 31.4 - - + -
78A CYS* 3.5 22.4 - - - -
80A LEU* 4.0 11.0 - - + +
92A LEU* 6.2 0.2 - - + -
106A ILE* 6.1 0.7 - - + -
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Residues in contact with CYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.8 5.8 - - - -
13A PHE* 4.1 13.5 - - - -
29A LEU* 5.3 3.1 - - - -
30A LEU* 1.3 83.9 - - - +
32A TYR* 1.3 61.8 + - - +
45A GLY 3.4 4.9 - - - -
46A TYR* 4.2 9.2 - - - -
77A THR 3.8 0.5 - - - +
78A CYS* 3.2 7.3 - - - -
79A TYR 3.1 40.9 + - - +
144A CYS* 3.8 16.4 - - - -
148A PHE* 3.5 38.7 - - + -
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.8 17.0 - - + +
31A CYS* 1.3 72.3 - - - +
33A GLN* 1.3 59.5 + - - +
34A LEU* 4.6 10.1 - - + -
43A THR* 5.0 6.5 - - - -
44A ARG* 3.5 10.0 + - - -
45A GLY* 2.9 75.3 + - - -
46A TYR 4.6 1.0 + - - -
47A PHE* 3.4 29.7 - + - -
59A PHE* 3.8 31.0 - + + -
62A GLU* 3.8 26.2 + - + +
63A ILE* 4.9 12.1 - - + -
76A VAL* 4.9 4.9 - - + -
77A THR 3.8 4.9 - - - +
78A CYS* 4.5 4.7 - - - -
148A PHE* 3.2 4.8 - - - -
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A CYS 5.0 0.2 - - - +
32A TYR* 1.3 72.1 - - - +
34A LEU* 1.3 61.8 + - - +
35A THR* 3.5 18.0 + - + +
42A PRO* 5.1 9.2 - - - +
43A THR 3.5 4.8 - - - +
44A ARG* 3.1 54.6 + - - +
76A VAL* 3.5 2.9 - - - +
77A THR* 2.8 54.0 + - + +
79A TYR* 6.5 0.4 - - + -
147A ASN* 5.0 7.8 - - - +
148A PHE* 3.8 17.7 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.9 10.2 - - + -
33A GLN* 1.3 71.2 - - - +
35A THR* 1.3 60.4 + - - +
36A PRO* 3.3 16.9 - - + +
42A PRO* 3.4 2.1 - - - +
43A THR* 2.9 54.8 + - - +
63A ILE* 4.3 23.3 - - + -
66A MET* 4.5 15.0 - - + -
68A LEU* 5.1 9.2 - - + -
74A TYR* 3.7 34.8 - - + -
76A VAL* 3.8 21.7 - - + +
102A LEU* 4.4 7.6 - - + -
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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