Contacts of the strand formed by residues 68 - 77 (chain A) in PDB entry 2CAR
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 VAL 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ILE* 3.9 4.2 - - - +
11A VAL* 3.3 21.1 - - + +
13A VAL* 3.8 22.9 - - + -
57A CYS* 4.0 11.0 - - - -
60A ALA* 3.9 22.4 - - + -
61A VAL* 3.8 29.4 - - + +
64A VAL* 4.3 12.6 - - + -
66A GLY 3.9 4.0 - - - +
67A PRO* 1.3 76.8 - - - +
69A LEU* 1.3 63.1 + - - +
70A VAL* 4.4 1.1 - - + -
119A ALA 3.7 0.7 - - - +
120A LEU* 3.4 6.1 - - - +
121A SER 2.9 32.0 + - - +
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Residues in contact with LEU 69 (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 ILE* 3.9 11.2 - - + -
11A VAL 2.8 12.7 + - - +
12A PHE* 3.6 20.0 - - + -
13A VAL* 3.0 27.0 + - - +
23A VAL* 5.2 2.9 - - + -
31A PHE* 6.1 0.2 - - + -
35A LEU* 4.1 24.2 - - + -
68A VAL* 1.3 74.5 - - - +
70A VAL* 1.3 64.3 + - - +
118A PHE* 4.1 30.5 - - + -
119A ALA 3.3 21.1 - - - +
120A LEU* 4.1 14.1 - - + -
185A LEU* 3.9 27.8 - - + -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.9 1.8 - - - -
13A VAL* 3.7 25.6 - - + -
42A LEU* 4.2 7.6 - - + -
53A SER 4.3 2.2 - - - +
56A LYS* 4.1 24.7 - - + -
57A CYS* 4.0 17.5 - - + +
60A ALA* 4.0 20.6 - - + -
68A VAL* 4.4 2.2 - - + -
69A LEU* 1.3 78.6 - - - +
71A GLU* 1.3 59.2 + - - +
72A ASP* 4.3 3.8 - - - +
117A THR 3.9 0.6 - - - +
118A PHE* 3.2 9.6 - - - -
119A ALA* 2.8 52.8 + - + +
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Residues in contact with GLU 71 (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 PHE* 4.1 14.2 - - + -
13A VAL 5.2 2.4 + - - +
56A LYS* 2.9 18.8 + - - +
70A VAL* 1.3 74.9 - - - +
72A ASP* 1.3 69.0 + - - +
73A THR* 4.0 8.6 + - - +
116A CYS* 3.5 14.6 - - - -
117A THR 3.5 4.0 - - - +
118A PHE* 3.4 26.6 - - + -
178A ARG* 2.7 56.2 + - - +
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Residues in contact with ASP 72 (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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44A GLU* 2.9 18.7 - - - +
52A ILE* 4.5 13.8 - - + +
53A SER* 4.0 23.4 + - - +
56A LYS* 2.7 43.5 + - - +
70A VAL* 4.3 4.5 - - - +
71A GLU* 1.3 74.4 + - - +
73A THR* 1.3 61.8 + - - +
74A CYS* 4.4 7.3 - - - -
115A LEU* 4.0 0.5 - - - +
116A CYS* 3.5 2.1 - - - -
117A THR* 2.8 34.7 + - - +
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Residues in contact with THR 73 (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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71A GLU* 4.0 15.9 + - - +
72A ASP* 1.3 75.1 + - - +
74A CYS* 1.3 72.7 + - - +
86A PRO* 5.1 2.8 - - - +
88A ILE* 3.8 15.6 - - - +
115A LEU 3.2 12.3 + - - +
116A CYS* 4.1 7.3 - - - +
151A TRP* 4.1 17.9 + - + +
177A HIS* 3.8 22.3 + - + +
178A ARG* 6.0 0.5 - - - +
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Residues in contact with CYS 74 (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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49A PRO* 4.1 12.6 - - - -
72A ASP* 5.5 6.3 - - - -
73A THR* 1.3 83.8 - - - +
75A LEU* 1.3 61.7 + - - +
76A CYS* 3.8 15.7 - - - -
85A GLY 3.4 11.4 - - - -
86A PRO* 3.6 34.1 - - - -
88A ILE* 4.5 0.9 - - - -
113A TYR 4.0 0.2 - - - +
114A ALA* 3.6 2.8 - - - +
115A LEU* 2.8 51.1 + - + +
117A THR* 6.1 0.4 - - - -
151A TRP* 4.8 0.2 - - - -
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Residues in contact with LEU 75 (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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74A CYS* 1.3 73.4 - - - +
76A CYS* 1.3 56.3 + - - +
77A PHE* 3.8 24.0 - - + -
84A PRO* 3.6 11.3 - - - +
85A GLY 2.8 30.7 + - - +
88A ILE* 3.9 27.9 - - + +
112A ALA* 4.9 1.3 - - + -
113A TYR 3.8 12.6 - - - +
114A ALA* 4.2 2.9 - - - -
140A ILE* 4.3 9.4 - - + -
151A TRP* 3.8 54.7 - - + -
154A CYS* 4.6 6.5 - - - -
155A PHE* 4.0 19.5 - - + -
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Residues in contact with CYS 76 (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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49A PRO* 5.5 4.7 - - - -
74A CYS* 3.8 23.6 - - - -
75A LEU* 1.3 77.0 - - - +
77A PHE* 1.3 62.8 + - - +
78A ASN 3.8 0.3 + - - -
82A GLY* 3.2 23.3 - - - +
85A GLY* 3.9 2.9 - - - -
112A ALA* 3.1 4.0 - - - -
113A TYR* 2.9 84.4 + - + +
115A LEU* 4.7 4.9 - - - -
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Residues in contact with PHE 77 (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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75A LEU* 3.8 17.7 - - + -
76A CYS* 1.3 75.8 - - - +
78A ASN* 1.3 66.4 + - - +
80A LEU* 3.1 32.7 + - + +
82A GLY* 3.1 18.6 + - - -
83A LEU 2.9 14.6 + - - +
84A PRO* 3.9 19.5 - - + -
100A LEU* 3.5 44.2 - - + -
103A LEU* 4.2 11.0 - - + -
104A LEU* 3.8 26.2 - - + -
111A SER 3.9 6.5 - - - +
112A ALA* 4.0 0.9 - - + -
140A ILE* 3.4 35.0 - - + -
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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