Contacts of the strand formed by residues 15 - 21 (chain A) in PDB entry 3VZC
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 CYS 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.4 15.7 - - - -
12A PRO* 3.1 23.8 - - + +
14A PRO* 1.3 73.4 - - - +
16A ARG* 1.3 62.7 + - - +
17A VAL* 4.9 4.7 - - - -
46A GLU 3.6 1.8 + - - +
47A ILE* 3.7 20.7 - - - -
48A SER* 3.1 24.6 + - - -
73A ASP* 3.0 27.4 - - + +
145A ARG* 3.4 19.3 - - - +
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Residues in contact with ARG 16 (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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15A CYS* 1.3 74.5 - - - +
17A VAL* 1.3 64.3 + - - +
48A SER* 3.4 20.4 - - - +
49A PHE* 5.6 0.2 - - - -
71A ARG* 3.3 26.9 - - - +
72A TRP* 4.2 13.2 - - + -
73A ASP* 2.9 44.2 + - - +
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Residues in contact with VAL 17 (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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11A LEU* 5.2 0.4 - - + -
15A CYS* 4.9 7.0 - - - -
16A ARG* 1.3 79.3 - - - +
18A LEU* 1.3 57.4 + - - +
19A VAL* 3.8 7.6 - - + -
42A LEU* 5.3 2.0 - - + -
47A ILE* 4.0 18.8 - - + -
48A SER 3.0 14.8 + - - +
49A PHE* 3.1 30.9 - - + +
50A THR 3.2 5.5 + - - -
72A TRP* 3.6 6.9 - - - -
73A ASP 5.0 0.2 - - - -
74A ALA* 3.4 33.2 - - + +
76A VAL* 3.5 26.9 - - + -
142A LEU* 4.6 9.6 - - + -
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Residues in contact with LEU 18 (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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17A VAL* 1.3 72.1 - - - +
19A VAL* 1.3 55.2 + - - +
20A LEU* 3.8 27.7 + - + +
50A THR* 3.6 16.8 - - - +
52A MET* 3.0 33.0 - - + -
63A LEU* 6.5 0.7 - - + -
64A VAL* 5.7 2.7 - - + -
67A GLU* 4.0 18.8 - - + +
72A TRP* 3.5 41.8 - - + +
74A ALA 3.0 7.1 + - - -
75A LEU* 3.4 23.9 - - + +
76A VAL 2.6 34.0 + - - +
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Residues in contact with VAL 19 (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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17A VAL* 3.8 15.9 - - + -
18A LEU* 1.3 71.7 - - - +
20A LEU* 1.3 70.7 + - - +
21A LEU 3.8 0.3 + - - -
34A PHE* 4.1 22.9 - - + -
42A LEU* 5.2 2.0 - - + -
49A PHE* 4.0 15.9 - - + -
50A THR 3.0 12.9 + - - +
51A LEU* 3.6 24.6 - - + +
52A MET* 2.9 28.4 + - - +
76A VAL* 3.2 30.7 - - + +
78A MET* 4.5 9.0 - - + -
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Residues in contact with LEU 20 (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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18A LEU* 3.8 26.9 - - + +
19A VAL* 1.3 72.5 - - - +
21A LEU* 1.3 56.4 + - - +
52A MET* 3.5 30.5 - - + +
54A THR* 4.2 11.0 - - + -
60A ALA* 4.2 19.7 - - + +
63A LEU* 5.0 10.5 - - + -
64A VAL* 4.2 18.2 - - + -
75A LEU* 5.8 4.9 - - + -
76A VAL 2.8 13.2 + - - +
77A VAL* 3.6 4.9 - - + -
78A MET* 2.8 32.4 + - - +
83A LEU* 3.8 10.3 - - + +
87A VAL* 4.1 23.8 - - + -
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Residues in contact with LEU 21 (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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19A VAL* 4.6 0.7 - - + -
20A LEU* 1.3 75.2 - - - +
22A ASN* 1.3 57.9 + - - +
23A PRO* 3.4 20.0 - - + +
30A ALA* 3.9 9.9 - - + +
31A LEU* 3.7 24.7 - - + +
34A PHE* 3.8 24.2 - - + -
51A LEU* 3.7 29.6 - - + -
52A MET 3.1 7.6 + - - +
53A LEU* 3.3 24.3 - - + -
54A THR* 2.8 31.6 + - - +
78A MET* 3.4 28.5 - - + +
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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