Contacts of the strand formed by residues 15 - 21 (chain D) in PDB entry 3VZD
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.3 16.4 - - - -
12D PRO* 3.3 23.8 - - + +
14D PRO* 1.3 74.8 - - - +
16D ARG* 1.3 62.2 + - - +
17D VAL* 4.9 4.9 - - - -
46D GLU 3.5 2.9 + - - +
47D ILE* 3.7 18.1 - - - -
48D SER* 3.0 26.2 + - - -
73D ASP* 3.0 28.5 - - + +
145D ARG* 3.7 17.0 - - - -
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Residues in contact with ARG 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D CYS* 1.3 76.3 - - - +
17D VAL* 1.3 62.3 + - - +
48D SER* 3.4 23.5 + - - -
71D ARG* 3.5 24.9 + - - +
72D TRP* 3.6 14.8 - - + -
73D ASP* 2.6 51.7 + - - +
74D ALA 3.7 0.5 + - - -
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Residues in contact with VAL 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 5.2 0.4 - - + -
15D CYS* 4.9 8.1 - - - -
16D ARG* 1.3 78.8 - - - +
18D LEU* 1.3 58.9 + - - +
19D VAL* 3.8 15.0 - - + -
42D LEU* 5.0 3.1 - - + -
47D ILE* 4.1 20.2 - - + -
48D SER 2.8 15.3 + - - +
49D PHE* 3.1 6.9 - - + -
50D THR 3.0 24.4 + - - -
72D TRP* 3.5 6.3 - - - -
74D ALA* 3.6 32.1 - - + +
76D VAL* 3.4 27.4 - - + -
142D LEU* 4.7 8.1 - - + -
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 1.3 72.2 - - - +
19D VAL* 1.3 60.4 + - - +
20D LEU* 3.7 21.8 + - + +
50D THR* 3.6 15.9 - - - +
52D MET* 3.1 38.6 - - + -
63D LEU* 4.8 2.2 - - + -
64D VAL* 5.9 3.1 - - + -
67D GLU* 3.8 25.6 - - + +
72D TRP* 3.4 40.2 - - + +
74D ALA 3.2 6.9 + - - -
75D LEU* 3.6 21.0 - - + +
76D VAL* 2.8 27.2 + - - +
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Residues in contact with VAL 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 3.8 20.2 - - + -
18D LEU* 1.3 75.5 - - - +
20D LEU* 1.3 67.9 + - - +
21D LEU* 3.7 4.0 + - + -
34D PHE* 4.3 18.4 - - + -
42D LEU* 5.1 2.2 - - + -
49D PHE* 4.1 14.6 - - + -
50D THR 2.7 14.8 + - - +
51D LEU* 3.4 24.9 - - + +
52D MET* 2.8 30.8 + - - +
76D VAL* 3.2 24.5 - - + +
78D MET* 4.6 8.3 - - + -
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Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.7 24.9 - - + +
19D VAL* 1.3 73.4 - - - +
21D LEU* 1.3 59.4 + - - +
52D MET* 3.6 26.9 - - + -
54D THR* 4.4 7.0 - - + -
60D ALA* 4.2 17.7 - - + +
63D LEU* 4.1 10.3 - - + -
64D VAL* 3.8 29.4 - - + -
75D LEU* 5.7 4.7 - - + -
76D VAL 2.7 13.6 + - - +
77D VAL* 3.6 5.3 - - + -
78D MET* 2.9 26.0 + - - +
83D LEU* 4.0 15.8 - - + +
87D VAL* 4.0 15.7 - - + -
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 4.6 1.1 - - + -
20D LEU* 1.3 74.8 - - - +
22D ASN* 1.3 60.6 + - - +
23D PRO* 3.2 26.7 - - + +
30D ALA* 3.5 23.8 - - + +
31D LEU* 3.7 15.0 - - + +
34D PHE* 3.8 29.8 - - + -
51D LEU* 3.9 23.8 - - + -
52D MET 3.0 10.7 + - - +
53D LEU* 3.4 16.5 - - + -
54D THR* 2.8 28.3 + - - +
78D MET* 3.6 24.2 - - + +
83D LEU* 5.4 0.2 - - - -
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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