Contacts of the strand formed by residues 15 - 21 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11F LEU* 4.6 11.7 - - - -
12F PRO* 3.3 22.2 - - + +
14F PRO* 1.3 76.5 - - - +
16F ARG* 1.3 57.9 + - - +
17F VAL* 4.4 9.9 - - - -
46F GLU 3.6 0.7 - - - +
47F ILE* 3.5 21.0 - - - -
48F SER* 2.9 25.1 + - - +
73F ASP* 3.1 28.7 - - + +
145F ARG* 3.5 17.0 - - - +
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Residues in contact with ARG 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E GLU* 5.9 4.4 + - - -
15F CYS* 1.3 73.0 - - - +
17F VAL* 1.3 64.4 + - - +
48F SER* 3.3 22.9 - - - +
49F PHE* 5.6 0.4 - - - -
50F THR* 6.3 0.2 - - + -
70F GLY 5.0 3.0 + - - -
71F ARG* 3.1 31.9 + - - +
72F TRP* 3.8 15.3 - - + -
73F ASP* 2.8 43.5 + - - +
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Residues in contact with VAL 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LEU* 5.5 0.7 - - + -
15F CYS* 4.4 11.2 - - - -
16F ARG* 1.3 82.4 - - - +
18F LEU* 1.3 63.4 + - - +
19F VAL* 3.6 2.4 + - + -
47F ILE* 4.1 20.4 - - + -
48F SER 2.8 11.8 + - - +
49F PHE* 3.2 7.1 - - + +
50F THR 3.2 23.4 + - - -
72F TRP* 3.7 5.6 - - - -
73F ASP 5.0 0.2 - - - -
74F ALA* 3.3 33.2 - - + +
76F VAL* 2.6 42.2 - - + +
142F LEU* 4.7 8.5 - - + -
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Residues in contact with LEU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F VAL* 1.3 71.6 - - - +
19F VAL* 1.3 56.2 + - - +
20F LEU* 3.7 30.2 + - + -
50F THR* 3.7 18.4 - - - +
52F MET* 3.8 30.7 - - + -
64F VAL* 5.7 3.1 - - + -
67F GLU* 4.3 15.0 - - + +
72F TRP* 3.5 48.9 - - + +
74F ALA 3.1 7.1 + - - -
75F LEU* 3.5 19.7 - - + +
76F VAL 2.8 32.1 + - - +
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Residues in contact with VAL 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F VAL* 4.2 1.3 - - + +
18F LEU* 1.3 71.7 - - - +
20F LEU* 1.3 62.2 + - - +
21F LEU* 3.4 9.9 + - + -
34F PHE* 3.9 32.5 - - + -
42F LEU* 5.4 2.9 - - + -
49F PHE* 3.9 27.4 - - + -
50F THR 3.2 10.5 + - - +
51F LEU* 3.6 15.0 - - + +
52F MET* 3.0 28.1 + - - +
76F VAL* 3.3 35.9 - - + +
78F MET* 4.5 5.4 - - + -
108F LEU* 6.1 0.2 - - + -
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F LEU* 3.7 27.1 + - + -
19F VAL* 1.3 71.1 - - - +
21F LEU* 1.3 54.0 + - - +
52F MET* 3.4 29.6 - - + +
54F THR* 4.7 8.3 - - + -
60F ALA* 4.2 8.7 - - + -
63F LEU* 4.7 13.2 - - + -
64F VAL* 3.8 17.7 - - + -
75F LEU* 5.6 4.7 - - + -
76F VAL 2.8 11.9 + - - +
77F VAL* 3.4 6.9 - - + -
78F MET 2.8 30.5 + - - -
83F LEU* 3.6 16.8 - - + +
87F VAL* 3.6 31.4 - - + -
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F VAL* 4.3 1.1 - - + -
20F LEU* 1.3 72.8 - - - +
22F ASN* 1.3 59.4 + - - +
23F PRO* 3.3 27.2 - - + +
30F ALA* 3.8 23.1 - - + +
31F LEU* 4.1 13.2 - - + -
34F PHE* 3.8 10.3 - - + -
51F LEU* 3.8 28.7 - - + -
52F MET 3.0 7.9 + - - +
53F LEU* 3.2 40.5 - - + -
54F THR* 3.4 5.2 + - - +
78F MET* 3.5 39.0 - - + +
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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