Contacts of the helix formed by residues 651 - 658 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H GLY* 3.6 24.5 - - - +
136H SER* 5.5 0.7 - - - -
644H THR 4.6 1.1 - - - +
647H ARG* 3.6 57.2 - - + +
649H GLY 3.9 2.0 - - - -
650H GLY* 1.3 86.5 - - - +
652H THR* 1.3 64.8 + - - +
653H HIS 3.1 0.7 + - - -
654H LEU* 3.3 4.6 + - - +
655H ALA* 3.0 23.1 + - - +
824H VAL* 5.7 0.3 - - - +
887H LEU* 6.0 2.5 - - + -
1001H GOL 4.4 11.4 - - - +
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Residues in contact with THR 652 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644H THR 4.3 1.1 + - - -
645H VAL* 3.0 28.0 - - - +
647H ARG 3.2 31.4 + - - +
648H GLY* 3.4 10.4 + - - +
650H GLY 3.1 0.2 - - - -
651H PRO* 1.3 75.0 - - - +
653H HIS* 1.3 60.9 + - - +
655H ALA* 4.2 7.2 - - - -
656H ILE* 2.9 31.3 + - - +
693H ARG* 3.0 30.9 - - - +
694H PHE* 4.1 17.0 - - + -
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Residues in contact with HIS 653 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H GLU* 3.2 40.3 + - - +
140H GLU* 3.1 26.0 - - - +
141H SER* 3.4 20.1 + - - -
146H THR* 4.6 2.4 + - - -
650H GLY 3.1 9.2 + - - +
651H PRO 3.1 0.8 - - - -
652H THR* 1.3 82.3 + - - +
654H LEU* 1.3 62.6 + - - +
656H ILE 3.4 0.2 + - - -
657H LEU* 3.2 31.0 + - + +
693H ARG* 3.6 20.4 - - + -
696H ALA* 4.0 11.4 - - + +
697H ALA* 3.5 30.5 - - + +
700H GLU* 4.6 6.7 - - - -
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Residues in contact with LEU 654 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H PHE* 3.5 47.1 - - + +
132H ALA* 4.7 4.5 - - - -
134H GLU* 3.0 21.0 + - + +
135H GLY* 4.1 13.0 - - - +
651H PRO* 3.3 5.7 + - + +
653H HIS* 1.3 76.2 - - - +
655H ALA* 1.3 60.3 + - - +
657H LEU* 3.1 10.6 + - + -
658H SER* 2.8 29.6 + - - -
820H PRO* 4.6 11.4 - - + -
823H ARG* 4.3 19.3 - - + -
824H VAL* 3.6 21.1 - - + -
827H ASP* 4.6 7.0 - - - +
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Residues in contact with ALA 655 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644H THR* 3.5 44.6 - - - +
645H VAL* 3.7 7.2 - - + +
651H PRO 3.0 17.0 + - - +
652H THR 3.8 3.4 - - - +
654H LEU* 1.3 76.8 - - - +
656H ILE* 1.3 59.6 + - - +
658H SER* 2.7 25.0 + - - -
659H GLN* 3.3 14.0 + - - -
824H VAL* 4.1 9.1 - - + +
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Residues in contact with ILE 656 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645H VAL* 3.8 18.8 - - + -
652H THR* 2.9 23.2 + - - +
655H ALA* 1.3 72.9 - - - +
657H LEU* 1.3 65.2 + - - +
658H SER 3.0 2.8 + - - -
659H GLN* 3.2 20.1 + - - +
664H ILE* 4.1 14.5 - - + +
668H ILE* 4.9 14.1 - - + -
670H VAL* 5.4 0.2 - - + -
693H ARG 4.9 0.2 - - - +
694H PHE* 3.7 37.0 - - + -
697H ALA* 3.7 28.9 - - + +
698H THR* 3.8 25.6 - - - +
701H HIS* 3.4 8.7 - - - -
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Residues in contact with LEU 657 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H PHE* 5.7 4.5 - - + -
134H GLU* 3.9 23.1 - - + +
653H HIS* 3.2 33.5 + - + +
654H LEU* 3.1 15.3 + - + +
656H ILE* 1.3 76.2 - - - +
658H SER* 1.3 58.9 + - - +
659H GLN 3.3 0.6 + - - -
697H ALA* 3.6 24.9 - - + +
700H GLU* 3.7 36.3 - - + +
701H HIS* 3.6 12.3 - - - +
704H HIS 5.2 3.8 - - - +
706H PRO* 3.4 27.7 - - - +
820H PRO* 4.9 1.9 - - + +
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Residues in contact with SER 658 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618H TYR* 4.1 13.0 - - - -
644H THR* 5.3 0.2 + - - -
654H LEU 2.8 14.0 + - - -
655H ALA* 2.7 17.8 + - - -
656H ILE 3.0 1.0 - - - -
657H LEU* 1.3 75.7 - - - +
659H GLN* 1.3 70.5 + - - +
660H PRO 3.8 0.5 - - - -
706H PRO* 4.2 4.5 - - - +
820H PRO* 3.6 39.5 - - - -
821H PHE* 3.8 10.8 + - - +
824H VAL* 3.8 14.9 - - - +
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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