Contacts of the helix formed by residues 677 - 682 (chain B) in PDB entry 5M7R
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 GLU 677 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A THR* 5.5 2.8 - - - +
253A LYS* 4.4 20.2 - - + +
569A TYR* 3.6 17.6 - - - -
672B LEU 6.1 0.5 - - - -
675B ASP 4.4 0.4 - - - -
676B GLN* 1.3 81.8 + - - +
678B PRO* 1.4 80.0 - - + +
679B TRP* 3.2 7.7 + - + +
680B ALA* 3.6 12.0 + - - +
681B PHE* 4.5 0.9 + - - -
712B SER* 3.0 41.2 + - - +
714B VAL* 5.9 2.5 - - + -
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Residues in contact with PRO 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A VAL* 4.9 5.4 - - + +
286A TYR* 3.8 40.4 - - + -
287A ASP* 5.4 1.4 - - - +
290A ARG* 4.3 6.2 + - - +
568A PRO* 6.5 0.9 - - + -
569A TYR* 3.7 18.4 - - + +
677B GLU* 1.4 91.0 - - + +
679B TRP* 1.3 56.9 + - - +
681B PHE* 3.0 25.9 + - + +
682B ARG* 3.5 13.9 + - - +
714B VAL* 4.2 26.2 - - + -
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Residues in contact with TRP 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690A GLN* 4.2 27.8 - - + +
693A LEU* 4.2 17.8 - - + +
694A PRO 3.2 29.2 - - - -
695A ILE* 3.6 39.6 - - + +
650B ILE* 6.2 1.4 - - + +
653B MET* 3.7 33.0 - - + +
672B LEU* 5.2 16.6 - - + -
677B GLU* 3.2 7.0 + - + +
678B PRO* 1.3 74.6 - - - +
680B ALA* 1.3 68.0 + - - +
682B ARG* 3.3 45.1 + - + +
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Residues in contact with ALA 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695A ILE* 5.5 6.6 - - - +
675B ASP 4.0 20.0 - - - +
676B GLN* 4.7 4.5 - - + -
677B GLU 3.6 8.9 + - - +
678B PRO 3.2 1.0 + - - -
679B TRP* 1.3 84.2 - - - +
681B PHE* 1.3 78.1 + - + +
682B ARG 3.8 0.7 + - - -
688B GLU* 5.1 4.0 - - - +
691B ARG* 4.3 12.1 + - - -
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Residues in contact with PHE 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ARG* 3.5 27.5 - - - +
568A PRO 3.6 13.0 - - - +
569A TYR* 3.4 40.6 - + - -
570A GLU* 4.0 3.6 - - - -
571A HIS* 3.9 36.3 - + - -
676B GLN* 4.1 22.2 - - + -
677B GLU 4.6 1.8 - - - -
678B PRO 3.0 9.1 + - - +
680B ALA* 1.3 93.2 - - + +
682B ARG* 1.3 65.6 + - - -
683B GLY 3.3 0.2 + - - -
684B GLY* 2.9 19.4 + - - +
688B GLU* 4.2 9.4 - - + -
691B ARG* 5.2 2.5 - - - +
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Residues in contact with ARG 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A TYR* 3.3 28.7 + - - -
287A ASP* 3.6 27.8 + - - +
690A GLN* 3.5 37.5 + - - +
289B LYS* 4.8 2.9 - - - +
645B TRP* 4.7 1.6 - - - -
646B ASP* 3.0 27.9 + - - -
649B SER* 4.5 11.1 + - - -
650B ILE* 3.5 21.8 - - - +
678B PRO* 3.5 10.2 + - - +
679B TRP* 3.3 47.5 + - + +
680B ALA 3.5 1.6 + - - -
681B PHE* 1.3 76.7 - - - +
683B GLY* 1.3 62.0 + - - +
684B GLY 3.4 3.8 + - - +
687B GLY* 4.2 0.3 - - - -
691B ARG* 3.3 28.1 + - - +
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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