Contacts of the strand formed by residues 365 - 369 (chain D) in PDB entry 6RIP
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 365 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360D TYR 5.0 1.2 + - - -
361D LEU* 3.8 24.6 - - + +
362D ARG* 3.1 48.1 + - + +
363D LEU 3.4 2.2 + - - -
364D HIS* 1.3 92.3 - - - +
366D CYS* 1.3 61.0 + - - +
437D PHE* 3.9 8.6 - - - -
438D GLU* 3.4 24.5 - - + +
440D VAL* 3.5 25.6 - - + +
450D HIS* 4.4 7.1 - - - +
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Residues in contact with CYS 366 (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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361D LEU* 4.2 3.8 - - - -
365D GLN* 1.3 75.2 - - - +
367D GLY* 1.3 79.6 + - - +
368D LEU* 5.0 2.9 - - - -
421D VAL* 4.9 6.1 - - - -
423D LEU* 4.0 26.2 - - + -
437D PHE* 3.6 35.8 - - + +
438D GLU 3.1 9.6 + - - +
439D PRO* 3.7 3.4 - - - +
440D VAL* 3.2 22.3 + - - -
448D GLN 3.5 8.7 - - - +
449D LEU* 4.7 6.7 - - + +
450D HIS 5.1 0.2 - - - +
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Residues in contact with GLY 367 (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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361D LEU* 3.9 7.8 - - - +
366D CYS* 1.3 92.7 - - - +
368D LEU* 1.3 64.1 + - - +
440D VAL* 3.7 10.1 - - - -
442D ILE* 4.4 6.7 - - - -
447D ILE* 4.0 5.5 - - - +
448D GLN* 2.4 41.0 + - - +
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Residues in contact with LEU 368 (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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366D CYS* 5.1 2.5 - - - -
367D GLY* 1.3 76.3 - - - +
369D PRO* 1.3 102.8 - - + +
372D MET* 4.8 3.4 - - + -
373D ALA* 3.6 24.7 - - + +
376D LEU* 5.2 9.6 - - + -
377D PHE* 6.2 2.0 - - + -
416D ILE* 5.8 1.6 - - + -
421D VAL* 4.4 19.7 - - + -
439D PRO* 4.0 31.0 - - + -
440D VAL 3.3 9.5 + - - +
441D LEU* 3.9 4.2 - - + -
442D ILE* 3.3 24.7 + - - +
446D ALA 5.3 1.6 - - - -
447D ILE* 4.8 4.0 - - + +
448D GLN* 4.4 2.0 - - - +
468D VAL* 4.8 18.4 - - + -
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Residues in contact with PRO 369 (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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1243C MET* 4.8 4.0 - - - -
353D SER* 4.9 0.2 - - - +
368D LEU* 1.3 100.2 - - + +
370D LYS* 1.3 67.5 + - - +
371D LYS 4.7 0.7 - - - +
372D MET* 3.6 42.0 - - + +
373D ALA* 3.3 13.7 + - - +
441D LEU* 5.0 0.7 - - - +
442D ILE* 3.8 6.3 - - + +
443D GLU 4.9 2.0 - - - +
444D GLY 4.3 3.6 - - - +
445D LYS* 4.1 35.0 - - + +
446D ALA 4.1 9.2 - - - +
447D ILE* 4.0 11.7 - - + +
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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