Contacts of the helix formed by residues 651 - 658 (chain A) in PDB entry 6V3O
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 PRO 651 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLY* 3.4 26.4 - - - +
136A SER* 5.3 0.9 - - - -
644A THR 4.7 0.7 - - - -
647A ARG* 3.3 41.7 - - + +
649A GLY 4.0 2.5 - - - -
650A GLY* 1.3 86.7 - - - +
652A THR* 1.3 62.3 + - - +
653A HIS 3.1 0.9 + - - -
654A LEU* 3.2 5.5 + - - +
655A ALA* 3.0 23.1 + - + +
824A VAL* 5.6 0.5 - - - +
1004A FLC 3.2 31.0 - - - +
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Residues in contact with THR 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A THR 4.3 3.8 + - - -
645A VAL 3.2 20.4 + - - +
647A ARG 2.2 39.8 + - - -
648A GLY* 3.1 9.8 + - - -
650A GLY 3.0 1.1 + - - -
651A PRO* 1.3 75.5 - - - +
653A HIS* 1.3 63.9 + - - +
655A ALA* 4.2 6.5 - - - -
656A ILE* 2.8 38.7 + - + +
693A ARG* 4.5 9.9 - - + -
694A PHE* 3.4 29.8 - - + -
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Residues in contact with HIS 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLU* 3.2 39.6 + - + +
140A GLU* 2.9 22.7 + - - +
141A SER* 3.3 25.6 - - - -
146A THR* 4.6 4.9 - - - +
650A GLY 3.0 11.5 + - - +
652A THR* 1.3 80.1 - - - +
654A LEU* 1.3 63.3 + - - +
657A LEU* 3.2 38.1 + - + +
693A ARG* 3.8 15.2 - - + +
696A ALA* 4.3 13.6 - - + +
697A ALA* 3.5 33.0 + - + +
700A GLU* 4.9 2.0 + - - -
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Residues in contact with LEU 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A PHE* 3.4 47.8 - - + +
132A ALA* 4.6 4.9 - - - +
134A GLU* 3.0 24.5 + - + +
135A GLY* 4.1 14.1 - - - +
651A PRO 3.2 5.9 + - - +
653A HIS* 1.3 71.5 - - - +
655A ALA* 1.3 60.5 + - - +
657A LEU* 2.9 11.8 + - + +
658A SER* 2.8 29.7 + - - -
820A PRO* 4.6 10.3 - - + -
823A ARG* 4.3 19.3 - - + -
824A VAL* 3.5 22.7 - - + -
827A ASP* 4.6 6.1 - - - +
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Residues in contact with ALA 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A THR* 3.4 44.6 - - - +
645A VAL* 3.8 6.1 - - + +
651A PRO* 3.0 17.0 + - + +
652A THR 3.7 3.8 - - - +
654A LEU* 1.3 77.5 - - - +
656A ILE* 1.3 60.7 + - - +
658A SER* 2.6 23.3 + - - -
659A GLN* 3.4 16.5 + - - -
824A VAL* 4.1 8.7 - - + +
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Residues in contact with ILE 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A VAL* 4.2 13.9 - - + -
652A THR* 2.8 40.5 + - + +
655A ALA* 1.3 71.9 - - - +
657A LEU* 1.3 66.9 + - - +
658A SER 3.1 2.7 + - - -
659A GLN* 3.3 17.9 + - - +
664A ILE* 3.9 19.3 - - + -
668A ILE* 4.6 14.1 - - + -
670A VAL* 5.3 0.2 - - + -
693A ARG 5.1 0.2 - - - +
694A PHE* 3.8 22.2 - - + -
697A ALA* 3.8 35.7 - - + +
698A THR* 3.8 15.9 - - - +
701A HIS* 3.4 11.3 - - + -
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Residues in contact with LEU 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A PHE* 5.7 4.0 - - + -
134A GLU* 3.8 23.8 - - + +
653A HIS* 3.2 34.8 + - + +
654A LEU* 2.9 15.3 + - + +
656A ILE* 1.3 76.7 - - - +
658A SER* 1.3 56.4 + - - +
659A GLN 3.3 0.6 + - - -
697A ALA* 3.7 24.2 - - + +
700A GLU* 3.8 33.9 - - + +
701A HIS* 3.6 12.6 - - - +
704A HIS 5.2 4.2 - - - +
706A PRO* 3.4 29.3 - - - +
820A PRO* 5.0 1.8 - - - -
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Residues in contact with SER 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618A TYR* 4.2 6.1 - - - -
644A THR* 5.2 0.3 + - - -
654A LEU 2.8 10.0 + - - -
655A ALA* 2.6 28.8 + - - -
656A ILE 3.1 0.2 - - - -
657A LEU* 1.3 76.0 - - - +
659A GLN* 1.3 66.4 + - - +
706A PRO* 4.3 4.7 - - - +
820A PRO* 3.5 40.8 - - - +
821A PHE* 3.8 18.4 + - - +
824A VAL* 3.7 12.4 - - - +
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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