Contacts of the strand formed by residues 10 - 14 (chain E) in PDB entry 3VXR
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 HIS 10 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D GLY 5.9 2.1 + - - -
8E PRO* 3.5 17.1 - - - +
9E ARG* 1.3 98.1 - - + +
11E LYS* 1.3 65.9 + - - +
12E ILE* 5.4 0.4 - - - -
109E ARG* 3.6 15.5 + - + +
153E HIS* 3.0 42.1 - + + +
154E VAL 5.3 0.8 + - - -
155E GLU* 2.7 32.9 + - - +
214E TYR* 3.4 51.1 - + + -
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Residues in contact with LYS 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E PRO* 4.2 11.0 - - + -
10E HIS* 1.3 78.7 - - - +
12E ILE* 1.3 76.3 + - - +
13E THR* 4.6 4.3 - - - -
18E ASN 5.5 1.1 - - - -
19E VAL* 3.8 35.4 - - + +
20E THR 6.0 0.4 - - - +
21E PHE* 4.0 23.8 - - + -
109E ARG 2.9 13.4 + - - +
110E LEU* 3.4 8.2 - - + +
111E THR 3.0 24.3 + - - -
153E HIS* 4.4 0.6 + - - -
217E SER* 4.8 15.8 - - - -
220E ASP* 5.5 4.4 + - - -
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Residues in contact with ILE 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E HIS* 5.1 0.2 - - + -
11E LYS* 1.3 87.5 + - - +
13E THR* 1.3 62.8 + - - +
111E THR* 3.4 9.2 - - - +
113E LEU* 3.8 28.7 - - + -
116E LEU* 4.4 12.7 - - + +
119E VAL* 4.7 6.5 - - + -
151E PRO* 4.1 16.8 - - + -
153E HIS* 3.8 31.4 - - + +
214E TYR* 3.1 41.3 - - + +
215E GLY* 4.1 19.1 + - - +
216E LEU* 5.6 2.0 - - + -
217E SER 5.8 0.3 + - - -
220E ASP* 5.1 6.4 - - - +
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Residues in contact with THR 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LYS* 4.0 5.8 - - - -
12E ILE* 1.3 75.4 - - - +
14E LYS* 1.3 65.0 + - - +
17E GLN* 3.3 24.3 - - - +
19E VAL* 4.0 19.5 - - + +
82E THR* 3.5 23.3 - - - +
110E LEU* 4.0 10.1 - - + -
111E THR 2.8 8.2 + - - +
112E VAL* 3.7 21.8 - - + -
113E LEU* 2.8 29.5 + - - +
116E LEU* 4.1 8.5 - - - +
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Residues in contact with LYS 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E THR* 1.3 79.9 + - - +
15E ARG* 1.3 77.5 + - - +
17E GLN* 2.9 41.6 + - - +
82E THR* 3.5 3.0 + - - -
112E VAL* 4.1 2.2 - - - -
113E LEU 3.4 3.8 - - - -
114E GLU 3.9 10.3 - - - +
115E ASP* 3.7 28.5 - - - -
116E LEU* 4.1 26.7 - - + +
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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