Contacts of the helix formed by residues 668 - 683 (chain H) in PDB entry 5A31
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 SER 668 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511H GLU 4.3 8.9 + - - -
513H SER* 5.8 2.0 - - - -
635H TYR* 4.4 2.3 + - - -
662H LEU* 4.1 0.7 - - - +
665H ASN* 2.8 36.9 + - - +
666H PRO 3.2 5.1 + - - -
667H GLN* 1.3 75.7 - - - +
669H SER* 1.3 65.1 + - - +
670H VAL* 4.4 7.6 - - - -
671H LEU* 3.6 33.2 - - - +
672H LEU* 3.3 24.3 + - - +
698H ILE* 3.8 0.7 - - - -
183L ILE* 4.8 1.4 - - - +
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Residues in contact with SER 669 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513H SER* 4.3 10.8 + - - -
667H GLN 3.3 5.3 + - - -
668H SER* 1.3 72.5 - - - +
670H VAL* 1.3 62.2 + - - +
672H LEU* 3.3 5.9 + - - +
673H CYS* 3.1 33.3 + - - -
695H ALA* 4.0 7.2 - - - +
698H ILE* 3.6 15.5 - - - -
699H ASP* 3.4 37.1 + - - +
702H ASN* 3.9 23.1 + - - -
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Residues in contact with VAL 670 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513H SER* 4.5 14.8 - - - +
515H TYR* 5.7 1.8 - - - +
639H TYR* 5.9 0.4 - - + -
668H SER* 4.4 7.9 - - - -
669H SER* 1.3 81.0 + - - +
671H LEU* 1.3 68.3 + - - +
673H CYS* 3.4 7.9 + - - +
674H HIS* 3.2 42.2 + - + -
702H ASN* 4.7 8.7 - - - +
704H LEU* 4.8 3.6 - - + -
180L TYR* 3.5 26.5 - - + +
181L ARG 4.5 1.6 - - - +
182L SER 4.7 1.1 - - - +
183L ILE* 3.6 48.0 - - + +
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Residues in contact with LEU 671 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635H TYR* 3.6 31.4 - - + -
639H TYR* 3.7 31.0 - - + -
658H PHE* 4.2 13.2 - - + +
661H ALA* 3.9 32.5 - - + +
662H LEU* 3.8 11.7 - - + +
665H ASN 4.3 5.2 - - - +
668H SER* 3.4 26.4 + - - +
669H SER 3.3 0.6 - - - -
670H VAL* 1.3 80.1 - - + +
672H LEU* 1.3 59.5 + - - +
674H HIS* 3.2 6.1 + - - +
675H ILE* 2.9 32.7 + - - +
183L ILE* 4.6 6.1 - - + -
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Residues in contact with LEU 672 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662H LEU* 3.6 33.2 - - + -
666H PRO 4.4 5.2 - - - +
668H SER 3.3 6.5 + - - +
669H SER 3.3 6.7 + - - +
671H LEU* 1.3 76.5 - - - +
673H CYS* 1.4 52.9 + - - +
675H ILE* 3.2 6.3 + - + +
676H GLY* 2.8 31.0 + - - -
691H THR* 3.4 34.1 - - + +
692H LEU* 5.1 0.6 + - - -
694H LYS* 4.2 22.7 - - + +
695H ALA* 3.7 20.4 - - + +
698H ILE* 3.3 34.1 - - + -
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Residues in contact with CYS 673 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669H SER 3.1 20.0 + - - -
670H VAL* 3.7 7.4 - - - +
671H LEU 3.3 0.2 - - - -
672H LEU* 1.4 73.3 - - - +
674H HIS* 1.3 59.3 + - - +
676H GLY* 3.3 1.7 + - - -
677H VAL* 2.9 36.3 + - - +
692H LEU* 4.1 13.7 - - + +
695H ALA* 4.1 1.6 - - - -
702H ASN* 4.0 5.8 - - - -
704H LEU* 4.3 16.4 - - + -
705H CYS* 3.3 45.8 - - - -
708H HIS* 4.4 7.9 - - + -
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Residues in contact with HIS 674 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639H TYR* 3.7 36.6 + + + -
643H MET* 4.8 11.0 - - + -
646H TYR* 6.3 1.2 - - - -
658H PHE* 4.2 24.8 - - + -
670H VAL* 3.2 30.3 + - + +
671H LEU* 3.4 10.1 - - - +
673H CYS* 1.3 80.9 - - + +
675H ILE* 1.3 62.7 + - - +
677H VAL* 3.2 9.0 + - - +
678H VAL* 3.0 28.4 + - - +
704H LEU* 5.1 4.9 - - + +
181L ARG 3.6 20.8 + - - -
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Residues in contact with ILE 675 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655H GLU* 5.0 8.3 - - + +
658H PHE* 3.7 28.0 - - + +
659H GLN* 3.9 15.3 - - + +
662H LEU* 3.7 46.0 - - + -
671H LEU* 2.9 23.4 + - + +
672H LEU* 3.5 10.1 - - + +
674H HIS* 1.3 72.0 - - - +
676H GLY* 1.3 58.1 + - - +
678H VAL* 3.2 9.7 + - - +
679H GLN* 2.9 54.3 + - + +
691H THR* 4.0 8.5 - - + -
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Residues in contact with GLY 676 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672H LEU 2.8 17.5 + - - -
673H CYS 3.6 3.4 - - - -
675H ILE* 1.3 73.9 - - - +
677H VAL* 1.3 56.8 + - - +
679H GLN* 3.1 2.5 + - - -
680H HIS* 2.9 26.2 + - - +
688H ALA* 3.4 19.5 - - - +
691H THR* 3.8 18.8 - - - +
692H LEU* 4.5 10.8 - - - -
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Residues in contact with VAL 677 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646H TYR* 3.9 24.0 - - + +
673H CYS 2.9 21.9 + - - +
674H HIS* 3.2 9.6 + - - +
676H GLY* 1.3 75.0 - - - +
678H VAL* 1.3 56.5 + - - +
680H HIS* 3.5 11.8 + - - +
681H ALA* 3.1 24.9 + - + +
692H LEU* 4.9 3.3 - - + +
708H HIS* 3.5 46.7 - - + +
712H VAL* 5.7 2.5 - - + -
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Residues in contact with VAL 678 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646H TYR* 3.8 24.9 - - + -
651H PHE* 3.3 35.0 - - + +
654H ALA* 4.1 3.6 - - + -
655H GLU* 3.6 21.1 - - + +
658H PHE* 3.8 24.2 - - + -
674H HIS* 3.0 16.9 + - - +
675H ILE* 3.5 7.4 - - - +
677H VAL* 1.3 73.8 - - - +
679H GLN* 1.3 65.3 + - - +
681H ALA* 3.0 8.3 + - - +
682H LEU* 3.0 21.7 + - + +
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Residues in contact with GLN 679 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655H GLU* 3.5 37.2 + - - +
659H GLN* 5.3 4.0 - - - +
675H ILE* 2.9 39.0 + - - +
676H GLY 3.1 6.3 + - - +
678H VAL* 1.3 75.4 - - - +
680H HIS* 1.3 62.4 + - - +
682H LEU* 3.2 6.1 + - - +
683H LYS 3.2 4.3 + - - -
684H LYS* 3.1 35.1 + - + +
687H LYS* 3.4 21.6 - - + +
688H ALA* 3.6 10.0 + - + -
691H THR* 2.9 24.6 + - - -
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Residues in contact with HIS 680 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676H GLY 2.9 12.1 + - - +
677H VAL* 3.6 12.7 + - - +
679H GLN* 1.3 76.8 - - - +
681H ALA* 1.3 60.8 + - - +
683H LYS* 3.1 27.1 + - + +
685H SER* 4.3 22.2 - - - +
688H ALA* 3.5 14.2 - - + +
711H SER* 5.7 4.5 - - - -
712H VAL* 4.2 26.8 - - + -
715H ALA* 3.5 30.1 - - + +
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Residues in contact with ALA 681 (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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646H TYR* 5.0 4.0 - - + +
651H PHE* 4.1 37.8 - - + -
677H VAL* 3.1 13.7 + - + +
678H VAL* 3.0 11.1 + - - +
680H HIS* 1.3 82.1 + - - +
682H LEU* 1.3 60.8 + - - +
683H LYS* 3.1 13.9 + - - +
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Residues in contact with LEU 682 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651H PHE* 3.2 37.9 - - + -
652H SER* 3.7 23.8 - - - +
655H GLU* 3.1 31.6 - - + +
678H VAL* 3.0 16.5 + - + +
679H GLN 3.2 7.8 + - - +
681H ALA* 1.3 73.7 - - - +
683H LYS* 1.3 71.4 + - - +
684H LYS* 3.3 20.6 + - - +
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Residues in contact with LYS 683 (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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679H GLN 3.2 0.2 + - - -
680H HIS* 3.1 23.3 + - + +
681H ALA 4.0 8.5 - - - +
682H LEU* 1.3 82.3 - - - +
684H LYS* 1.3 56.7 + - - +
685H SER* 3.0 20.2 + - - +
686H GLU* 4.8 2.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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