Contacts of the strand formed by residues 33 - 38 (chain N) in PDB entry 1VQN
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 ARG 33 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30069 C 2.8 31.8 + - - -
30079 G 3.2 17.2 + - - -
23N ARG* 3.8 14.3 - - - +
26N LEU* 4.0 32.3 - - + +
27N LEU* 4.2 18.6 - - + +
31N LYS 3.7 5.6 + - - +
32N PRO* 1.3 74.5 - - - +
34N LEU* 1.3 60.0 + - - +
35N VAL* 3.4 9.5 + - + +
46N GLN 3.3 1.0 - - - +
47N LEU* 3.2 6.7 - - - -
48N VAL* 2.7 46.6 + - - +
55N ASP* 3.3 25.5 + - - -
101N VAL* 3.5 9.9 - - + +
103N ASP* 2.5 42.9 + - + -
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Residues in contact with LEU 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N PRO 3.9 1.0 + - - -
33N ARG* 1.3 70.7 - - - +
35N VAL* 1.3 60.4 + - - +
36N ALA 3.2 3.6 + - - -
45N ALA* 4.5 18.8 - - + -
46N GLN 3.3 4.7 - - - +
47N LEU* 3.5 27.8 - - + -
88N ALA* 5.5 1.3 - - + -
100N ALA* 4.1 13.5 - - + -
101N VAL 3.0 15.0 + - - +
102N LEU* 3.8 23.4 - - + +
103N ASP 3.2 17.3 + - - +
118N ILE* 4.7 7.0 - - + -
119N GLN* 4.2 13.9 - - + -
122N ALA* 3.8 20.0 - - + -
127N LEU* 5.5 0.2 - - + -
129N ILE* 3.8 23.3 - - + -
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Residues in contact with VAL 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30069 C 3.5 28.3 - - - +
33N ARG* 4.2 19.7 - - + +
34N LEU* 1.3 67.7 - - - +
36N ALA* 1.3 58.6 + - - +
37N ARG* 3.5 34.1 - - + +
44N ARG* 3.6 2.1 - - - +
45N ALA* 3.4 4.7 - - - -
46N GLN* 2.7 49.8 + - + +
48N VAL* 3.4 33.0 - - + -
103N ASP* 3.6 6.5 - - - +
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Residues in contact with ALA 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34N LEU* 3.2 1.5 + - + +
35N VAL* 1.3 71.2 - - - +
37N ARG* 1.3 81.2 + - - +
44N ARG 3.6 3.8 - - - -
45N ALA* 4.7 0.9 - - - +
102N LEU* 4.1 19.7 - - + -
103N ASP 3.0 15.0 + - - +
104N ILE* 4.1 7.0 - - - +
107N ASN* 4.5 2.3 - - - +
115N VAL* 4.3 17.1 - - + +
118N ILE* 3.7 27.6 - - + -
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Residues in contact with ARG 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30059 G 3.8 26.2 - - - +
30069 C 2.7 53.9 + - - -
30079 G 4.7 3.6 + - - -
17N ARG 5.3 1.4 + - - -
35N VAL* 3.5 17.8 - - + +
36N ALA* 1.3 92.6 + - - +
38N LYS* 1.3 67.6 + - - +
43N VAL* 3.6 7.3 - - - +
44N ARG* 2.8 40.4 + - + +
103N ASP* 2.6 40.4 + - - -
104N ILE 3.8 0.6 - - - -
105N GLY* 2.9 25.4 - - - +
106N LEU 5.5 0.4 - - - +
107N ASN* 4.3 2.0 - - - -
118N ILE* 4.2 1.8 - - - +
9307N CL 3.2 24.2 - - + -
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Residues in contact with LYS 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30289 U 4.1 4.0 + - - -
30479 A 4.1 15.4 + - - -
30489 C 2.7 31.0 + - - +
146D LYS* 3.5 16.1 + - - +
37N ARG* 1.3 81.5 - - - +
39N SER* 1.3 66.5 + - - +
42N HIS 3.5 9.0 - - - +
43N VAL* 4.3 11.7 - - + +
44N ARG 4.8 0.2 - - - +
107N ASN* 3.0 34.8 - - - +
114N LYS* 4.4 20.8 - - + +
115N VAL* 4.4 13.7 - - + -
118N ILE* 6.2 0.4 - - + -
9307N CL 3.6 12.9 - - - +
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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