Contacts of the helix formed by residues 651 - 658 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLY* 3.4 26.7 - - - +
136B SER* 5.3 1.1 - - - -
644B THR 4.7 0.9 - - - -
647B ARG* 3.4 37.9 - - - +
649B GLY 3.9 2.5 - - - -
650B GLY* 1.3 88.7 - - - +
652B THR* 1.3 61.7 + - - +
653B HIS 3.1 0.7 + - - -
654B LEU* 3.3 5.7 + - - +
655B ALA* 3.0 21.1 + - - +
824B VAL* 5.7 0.5 - - - +
884B ASP* 5.9 1.6 - - - +
1004B FLC 3.0 33.0 - - + +
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Residues in contact with THR 652 (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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644B THR 4.2 3.6 - - - -
645B VAL* 3.0 26.9 + - - +
647B ARG* 3.1 19.8 + - - +
648B GLY* 3.6 11.7 - - - -
650B GLY 4.1 0.2 - - - +
651B PRO* 1.3 76.2 - - - +
653B HIS* 1.3 66.3 + - - +
655B ALA* 3.7 8.2 - - - +
656B ILE* 2.9 32.9 + - + +
693B ARG* 3.4 31.4 - - + -
694B PHE* 3.5 20.3 - - + -
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Residues in contact with HIS 653 (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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134B GLU* 3.2 41.8 + - + +
140B GLU* 2.8 23.0 + - + +
141B SER 3.3 24.9 - - - -
146B THR* 4.9 2.5 + - - -
650B GLY 3.0 10.5 + - - +
652B THR* 1.3 82.5 - - - +
654B LEU* 1.3 63.0 + - - +
656B ILE 3.4 0.2 + - - -
657B LEU* 3.2 30.9 + - + +
693B ARG* 3.9 13.6 - - + +
696B ALA* 4.4 12.6 - - + +
697B ALA* 3.5 32.3 + - + +
700B GLU* 4.7 5.5 + - - -
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Residues in contact with LEU 654 (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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131B PHE* 3.5 46.0 - - + +
132B ALA* 4.7 2.2 - - - +
134B GLU* 3.0 24.7 + - + +
135B GLY* 4.0 13.7 - - - +
651B PRO 3.3 5.3 + - - +
653B HIS* 1.3 75.6 - - - +
655B ALA* 1.3 63.9 + - - +
657B LEU* 3.1 10.8 + - + -
658B SER* 2.9 21.8 + - - -
820B PRO* 4.5 9.9 - - + -
823B ARG* 3.8 29.6 - - + -
824B VAL* 3.6 18.2 - - + -
827B ASP* 4.7 4.9 - - - +
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Residues in contact with ALA 655 (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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644B THR* 3.5 43.9 + - - +
645B VAL* 3.7 6.7 - - + +
651B PRO 3.0 16.6 + - - +
652B THR 3.2 4.2 + - - +
654B LEU* 1.3 77.6 - - - +
656B ILE* 1.3 61.1 + - - +
658B SER* 2.7 23.2 + - - -
659B GLN* 3.3 16.1 + - - -
824B VAL* 4.1 8.7 - - + +
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Residues in contact with ILE 656 (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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645B VAL* 3.5 22.0 - - + -
652B THR* 2.9 31.3 + - - +
655B ALA* 1.3 72.8 - - - +
657B LEU* 1.3 66.9 + - - +
658B SER 3.0 3.1 + - - -
659B GLN* 3.2 21.0 + - - +
664B ILE* 3.9 20.8 - - + +
668B ILE* 4.8 9.6 - - + -
694B PHE* 3.8 24.7 - - + +
697B ALA* 3.8 26.5 - - + +
698B THR* 3.9 24.5 - - - +
701B HIS* 3.4 8.7 - - + -
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Residues in contact with LEU 657 (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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131B PHE* 5.7 4.5 - - + -
134B GLU* 3.9 22.0 - - + -
653B HIS* 3.2 32.0 + - + +
654B LEU* 3.1 16.2 + - + +
656B ILE* 1.3 77.7 - - - +
658B SER* 1.3 56.0 + - - +
697B ALA* 3.7 18.6 - - + +
700B GLU* 3.6 40.4 - - + +
701B HIS* 3.5 13.8 - - - +
704B HIS 5.1 4.6 - - - +
706B PRO* 3.4 29.8 - - - +
820B PRO* 5.0 2.0 - - + +
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Residues in contact with SER 658 (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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618B TYR* 4.2 12.5 - - - -
654B LEU 2.9 13.2 + - - -
655B ALA* 2.7 22.7 + - - -
656B ILE 3.0 0.8 - - - -
657B LEU* 1.3 73.1 - - - +
659B GLN* 1.3 70.7 + - - +
660B PRO 3.7 0.7 - - - -
706B PRO* 4.1 6.4 - - - +
820B PRO* 3.5 41.1 - - - -
821B PHE* 3.7 9.9 + - - +
824B VAL* 3.8 13.7 - - - +
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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