Contacts of the strand formed by residues 67 - 73 (chain R) in PDB entry 4V1N
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 GLN 67 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372Q SER* 5.4 4.5 - - - -
373Q VAL 5.5 1.9 + - - -
65R ASN 3.6 4.1 + - - +
66R ARG* 1.4 77.0 - - - +
68R VAL* 1.4 62.0 + - - +
216R GLY* 5.5 0.4 - - - -
217R THR* 3.5 5.2 - - - +
219R CYS* 3.7 23.6 - - + -
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Residues in contact with VAL 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370Q LEU* 5.5 6.7 - - + -
371Q LEU 3.6 16.2 - - - +
372Q SER* 5.0 6.5 - - - +
67R GLN* 1.4 75.5 - - - +
69R TRP* 1.4 63.8 + - - +
134R VAL* 6.0 5.8 - - + -
216R GLY* 5.5 4.9 - - - -
217R THR 3.0 14.0 + - - +
218R VAL* 3.5 5.6 - - + -
219R CYS* 3.0 26.2 + - - +
220R HIS 3.8 2.1 + - - -
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Residues in contact with TRP 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370Q LEU* 3.5 6.1 - - - +
371Q LEU* 2.8 46.3 + - + +
68R VAL* 1.4 77.2 - - - +
70R LEU* 1.3 63.0 + - - +
71R VAL* 4.0 1.8 - - + -
218R VAL* 5.4 0.9 - - - -
220R HIS* 3.4 18.8 - - + +
222R CYS* 6.2 2.7 - - + -
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Residues in contact with LEU 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368Q TYR* 5.7 6.3 - - + -
369Q VAL 3.7 5.8 - - - +
370Q LEU* 4.9 1.1 - - - +
68R VAL 4.4 0.2 + - - -
69R TRP* 1.3 72.9 - - - +
71R VAL* 1.3 60.6 + - - +
218R VAL* 4.8 13.8 - - + +
220R HIS 3.1 11.2 + - - +
221R GLU* 3.4 8.8 - - + +
222R CYS* 3.0 25.8 + - - +
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Residues in contact with VAL 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368Q TYR* 3.3 5.0 - - - +
369Q VAL* 2.8 42.1 + - + +
371Q LEU* 5.7 7.0 - - + -
69R TRP* 4.0 3.3 - - + +
70R LEU* 1.3 74.8 - - - +
72R ARG* 1.3 63.2 + - - +
73R LEU* 3.7 2.4 + - + +
222R CYS* 3.3 15.0 - - + +
224R VAL* 5.5 4.5 - - + +
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Residues in contact with ARG 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366Q ASP* 5.0 10.1 - - + -
367Q SER 3.4 7.9 - - - +
368Q TYR* 4.4 4.0 - - + +
71R VAL* 1.3 72.1 - - - +
73R LEU* 1.3 60.1 + - - +
222R CYS 3.0 14.0 + - - +
223R GLN* 4.2 12.6 - - + -
224R VAL* 2.8 31.5 + - - +
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Residues in contact with LEU 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366Q ASP* 3.2 5.9 - - - +
367Q SER* 2.7 36.1 + - - +
369Q VAL* 5.7 7.4 - - + -
71R VAL* 3.7 3.8 + - + +
72R ARG* 1.3 74.5 - - - +
74R PRO* 1.3 69.2 - - - +
77R LEU* 5.0 8.3 - - + -
78R ALA* 5.2 9.3 - - + +
224R VAL* 4.5 9.6 - - + -
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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