Contacts of the strand formed by residues 49 - 56 (chain A) in PDB entry 4CSY
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 TYR 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A THR* 3.5 31.3 + - + +
42A LEU* 3.8 10.5 - - + +
43A SER* 2.7 38.4 + - - -
45A SER* 4.6 7.2 - - - -
48A TYR* 1.3 86.1 - + - +
50A TRP* 1.3 60.7 + - - +
92A GLU* 3.2 6.9 - - - -
93A ILE* 2.9 37.9 + - + +
95A ILE* 3.6 35.4 - - + -
113A LYS* 4.5 1.3 - - - -
114A LEU* 3.3 48.8 - - + +
116A LEU* 3.9 20.4 - - + -
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Residues in contact with TRP 50 (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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10A MET 2.9 27.6 + - - -
11A THR 3.9 0.9 - - - -
12A TYR* 3.3 31.8 - + + +
15A ALA* 3.6 27.6 - - + -
26A LEU* 3.7 7.6 - - + +
49A TYR* 1.3 71.6 - - - +
51A ILE* 1.3 62.5 + - - +
90A CYS* 3.6 24.7 - - + -
91A VAL 3.4 20.6 - - - -
92A GLU 4.2 0.7 - - - -
107A GLU* 3.9 11.2 - - + -
108A ARG 3.3 24.9 - - - -
109A CYS 3.9 7.2 - - - -
111A LYS 3.2 19.5 + - - -
113A LYS* 3.6 47.5 - - + +
114A LEU 3.0 9.8 + - - +
116A LEU* 3.4 22.5 + - - +
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Residues in contact with ILE 51 (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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12A TYR* 2.9 23.8 + - - -
26A LEU* 4.0 6.1 - - - -
27A VAL* 3.4 30.7 - - + +
30A GLN* 3.9 9.4 - - - +
49A TYR 4.2 0.2 - - - +
50A TRP* 1.3 74.9 - - - +
52A GLY* 1.3 58.5 + - - +
53A ILE* 2.9 26.7 + - + -
91A VAL* 3.1 34.1 + - + +
92A GLU 4.6 1.1 - - - -
93A ILE* 3.5 33.9 - - + -
104A TRP* 3.7 29.8 - - + +
116A LEU* 4.3 1.1 - - + -
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Residues in contact with GLY 52 (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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12A TYR* 3.5 9.9 - - - -
26A LEU* 3.6 15.1 - - - +
27A VAL 2.9 21.3 + - - -
28A ALA* 5.0 2.2 - - - +
51A ILE* 1.3 68.8 - - - +
53A ILE* 1.3 59.8 + - - +
62A TRP* 3.5 11.6 - - - -
63A VAL* 2.8 38.3 + - - +
64A GLY 4.8 0.2 + - - -
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Residues in contact with ILE 53 (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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12A TYR* 3.4 6.5 + - - -
51A ILE* 2.9 24.3 + - + +
52A GLY* 1.3 72.5 - - - +
54A ARG* 1.4 66.1 + - - +
60A TRP* 4.0 9.9 - - + -
61A VAL 3.3 12.3 - - - +
62A TRP* 3.4 38.4 - - + -
69A LEU* 3.9 20.9 - - + -
91A VAL* 3.2 43.8 + - + +
104A TRP* 3.5 41.3 - - + -
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Residues in contact with ARG 54 (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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12A TYR* 3.6 20.9 - - - +
13A ASP* 3.2 29.5 + - - -
16A SER* 6.1 0.2 - - - -
53A ILE* 1.4 76.2 - - - +
55A LYS* 1.3 64.5 + - - +
56A VAL* 3.7 16.2 + - + -
60A TRP* 3.6 8.5 - - - -
61A VAL* 2.9 33.5 + - + +
63A VAL* 3.7 23.1 - - + +
89A ASP* 3.3 14.0 + - - +
90A CYS* 3.7 8.6 - - - -
109A CYS* 3.7 27.7 - - - +
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Residues in contact with LYS 55 (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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54A ARG* 1.3 75.4 + - - +
56A VAL* 1.3 64.1 + - - +
57A ASN 4.3 0.4 - - - -
58A ASN* 3.7 41.3 - - + +
59A VAL 3.4 6.5 - - - +
60A TRP* 3.4 31.2 - - + +
83A ASN* 3.8 24.4 - - - +
88A GLU 3.4 15.4 + - - -
89A ASP* 2.8 52.2 + - + +
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Residues in contact with VAL 56 (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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54A ARG* 4.0 13.7 - - + +
55A LYS* 1.3 78.9 - - - +
57A ASN* 1.4 77.7 + - - +
58A ASN 3.2 0.2 - - - -
59A VAL* 2.8 30.3 + - - +
61A VAL* 3.8 32.6 - - + +
66A GLN* 4.4 18.4 - - - +
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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