Contacts of the strand formed by residues 56 - 65 (chain A) in PDB entry 5V5W
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 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A TYR* 3.5 29.6 - - + -
50A ILE* 3.6 4.9 - - + +
54A ASP 3.9 0.8 + - - -
55A THR* 1.3 72.8 - - - +
57A MET* 1.3 72.4 + - - +
58A LEU* 3.9 19.3 - - + -
93A LEU* 4.0 25.4 - - + +
94A ARG* 3.3 2.6 - - - +
95A ILE* 2.8 46.6 + - + +
98A ILE* 3.8 20.6 - - + -
106A TYR* 5.2 3.4 - - + -
124A VAL* 3.6 37.5 - - + -
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Residues in contact with MET 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 2.9 40.0 + - + +
33A GLY* 3.6 24.5 - - - +
48A TYR* 3.1 13.7 + - - -
55A THR* 3.8 2.4 + - + -
56A LEU* 1.3 82.5 - - - +
58A LEU* 1.3 62.2 + - - +
59A GLN* 5.5 3.6 - - - +
92A THR* 3.5 24.5 - - + -
93A LEU 3.2 9.6 - - - +
94A ARG* 3.4 38.8 - - + +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.5 7.4 - - + -
30A VAL 3.9 1.3 - - - -
31A HIS* 4.4 7.6 - - - -
48A TYR* 3.4 38.4 - - + -
56A LEU* 3.9 18.8 - - + -
57A MET* 1.3 75.4 - - - +
59A GLN* 1.3 64.4 + - - +
72A TRP* 3.8 28.7 - - + -
91A GLU 3.8 1.9 - - - +
92A THR* 3.5 3.5 - - - +
93A LEU* 3.0 41.5 + - + -
106A TYR* 4.5 3.4 - - + -
122A ILE* 3.7 30.7 - - + -
124A VAL* 4.5 10.5 - - + -
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Residues in contact with GLN 59 (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 ILE* 3.2 9.0 - - - +
30A VAL* 2.9 53.8 + - + +
31A HIS 4.9 2.0 + - - -
32A ALA* 3.9 22.8 - - + +
57A MET* 5.5 3.4 - - - +
58A LEU* 1.3 76.5 - - - +
60A CYS* 1.3 61.6 + - - +
61A LEU* 3.9 19.3 - - + +
72A TRP* 4.2 1.8 - - - -
91A GLU* 4.2 15.3 - - - +
92A THR* 4.1 19.0 + - + +
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Residues in contact with CYS 60 (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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27A ALA* 4.0 19.1 - - - -
28A GLN 3.4 8.7 - - - -
29A ILE* 4.7 0.4 - - - -
59A GLN* 1.3 73.4 - - - +
61A LEU* 1.3 64.8 + - - +
62A VAL* 3.7 15.1 + - - +
70A VAL* 3.9 13.3 - - + +
72A TRP* 4.0 6.7 - - + -
91A GLU* 3.5 32.4 + - - +
108A CYS* 2.0 48.5 - - - -
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Residues in contact with LEU 61 (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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26A GLN 3.9 0.3 - - - +
27A ALA* 3.6 1.0 - - - -
28A GLN* 2.9 52.7 + - - +
30A VAL* 3.5 28.9 - - + -
59A GLN* 4.0 20.6 - - + +
60A CYS* 1.3 73.8 - - - +
62A VAL* 1.3 60.7 + - - +
63A THR* 5.4 2.1 - - + +
91A GLU* 4.3 18.4 - - - +
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Residues in contact with VAL 62 (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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26A GLN 3.1 14.4 - - - +
60A CYS* 3.8 14.1 - - - +
61A LEU* 1.3 80.1 - - - +
63A THR* 1.3 67.7 + - - +
67A ARG* 6.1 0.7 - - + -
68A PRO* 3.9 35.3 - - + +
70A VAL* 3.7 21.3 - - + -
110A ALA* 3.6 20.9 - - + -
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Residues in contact with THR 63 (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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25A ALA* 3.5 0.3 - - - -
26A GLN* 3.0 47.9 + - + +
61A LEU* 5.4 1.8 - - + +
62A VAL* 1.3 80.6 - - - +
64A GLY* 1.3 65.3 + - - +
68A PRO* 3.0 21.5 - - - +
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Residues in contact with GLY 64 (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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23A ALA* 3.7 11.2 - - - -
24A PRO 3.7 17.0 - - - -
63A THR* 1.3 82.2 + - - +
65A HIS* 1.3 77.2 + - - -
66A PRO 3.1 15.9 - - - +
67A ARG* 3.9 2.3 - - - -
68A PRO* 3.6 4.5 - - - +
112A ASN* 4.0 1.6 - - - -
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Residues in contact with HIS 65 (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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22A TYR* 3.3 14.2 - - - +
23A ALA* 2.8 46.7 + - + +
64A GLY* 1.3 87.7 + - - -
66A PRO* 1.3 69.7 - - + +
67A ARG* 5.2 1.2 + - - -
112A ASN* 3.7 1.9 + - - -
114A VAL* 3.8 0.7 - - - +
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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