Contacts of the helix formed by residues 621 - 640 (chain u) in PDB entry 6FF7
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 ASP 621 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619u ASN* 3.3 9.7 - - + +
620u MET* 1.3 78.4 - - - +
622u GLU* 1.3 64.4 + - - +
623u TYR* 3.3 7.6 - - + +
624u VAL* 3.9 14.2 + - + +
625u ARG* 3.4 20.3 + - - +
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Residues in contact with GLU 622 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620u MET 3.5 4.8 + - - +
621u ASP* 1.3 71.0 - - - +
623u TYR* 1.3 60.2 + - - +
625u ARG* 3.8 6.9 - - - +
626u ASN* 2.9 32.6 + - - +
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Residues in contact with TYR 623 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621u ASP* 3.3 5.1 - - + -
622u GLU* 1.3 77.8 - - - +
624u VAL* 1.3 57.2 + - - +
626u ASN* 3.9 3.9 - - - +
627u THR* 3.0 31.2 + - - -
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Residues in contact with VAL 624 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579u GLU* 6.3 1.6 - - - -
616u ASP* 4.2 11.1 - - + +
619u ASN* 5.7 6.1 - - + -
621u ASP* 3.9 14.6 + - + +
623u TYR* 1.3 79.7 - - - +
625u ARG* 1.3 56.6 + - - +
627u THR* 4.5 4.5 - - - +
628u THR* 2.8 32.4 + - - -
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Residues in contact with ARG 625 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616u ASP 3.9 16.1 + - - +
617u ILE* 4.7 11.4 - - - +
619u ASN* 4.9 4.7 - - + +
621u ASP 3.4 17.6 + - - +
622u GLU* 3.8 7.2 - - - +
623u TYR 3.2 0.4 - - - -
624u VAL* 1.3 76.4 - - - +
626u ASN* 1.3 59.6 + - - +
628u THR* 3.4 1.6 + - - -
629u ALA* 3.0 28.9 + - - +
663u THR* 5.3 10.0 - - - -
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Residues in contact with ASN 626 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622u GLU 2.9 18.6 + - - +
623u TYR* 3.9 4.0 - - - +
625u ARG* 1.3 75.0 - - - +
627u THR* 1.3 58.3 + - - +
629u ALA* 3.3 8.0 + - - +
630u ARG* 3.0 26.0 + - - +
666u LYS* 6.0 2.2 - - - -
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Residues in contact with THR 627 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579u GLU* 4.3 32.8 - - - +
582u LEU* 5.5 4.5 - - - -
583u ILE* 6.0 5.8 - - - -
623u TYR 3.0 19.6 + - - -
624u VAL* 4.2 4.3 - - - -
626u ASN* 1.3 74.3 - - - +
628u THR* 1.3 59.8 + - - +
630u ARG* 3.3 8.7 + - - +
631u ALA* 2.9 26.3 + - - +
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Residues in contact with THR 628 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613u MET* 5.2 12.1 - - - +
616u ASP* 4.0 28.5 - - - -
624u VAL 2.8 21.0 + - - -
625u ARG 3.8 3.6 - - - -
627u THR* 1.3 75.0 - - - +
629u ALA* 1.3 58.5 + - - +
631u ALA* 3.1 9.1 + - - +
632u PHE* 2.9 27.9 + - - +
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Residues in contact with ALA 629 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625u ARG 3.0 17.0 + - - +
626u ASN* 3.5 6.7 - - - +
628u THR* 1.3 77.0 - - - +
630u ARG* 1.3 57.1 + - - +
632u PHE* 3.3 9.0 + - - +
633u ALA* 3.0 26.5 + - - +
663u THR* 3.9 26.9 - - - +
666u LYS* 4.0 18.2 - - + +
667u ILE* 4.1 10.5 - - - +
670u GLN* 5.0 0.4 - - - +
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Residues in contact with ARG 630 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582u LEU* 5.3 12.6 - - + -
626u ASN 3.0 12.9 + - - +
627u THR* 3.5 11.2 - - - +
628u THR 3.3 0.2 - - - -
629u ALA* 1.3 75.7 - - - +
631u ALA* 1.3 57.0 + - - +
633u ALA* 3.2 8.9 + - - +
634u VAL* 2.9 28.8 + - - +
670u GLN* 4.6 10.5 - - + +
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Residues in contact with ALA 631 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575u LEU* 6.6 0.4 - - + -
597u ILE* 6.0 7.5 - - + +
613u MET* 6.1 4.7 - - + -
627u THR 2.9 14.5 + - - +
628u THR* 3.1 13.0 + - - +
630u ARG* 1.3 74.5 - - - +
632u PHE* 1.3 59.2 + - - +
634u VAL* 3.3 4.8 + - - +
635u VAL* 3.0 30.3 + - - +
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Residues in contact with PHE 632 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613u MET* 6.6 0.2 - - + -
628u THR 2.9 13.6 + - - +
629u ALA* 3.3 12.1 + - - +
631u ALA* 1.3 76.1 - - - +
633u ALA* 1.3 57.0 + - - +
635u VAL* 3.5 3.3 + - - +
636u ALA* 2.9 30.5 + - - +
667u ILE* 4.5 13.0 - - + -
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Residues in contact with ALA 633 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629u ALA 3.0 13.6 + - - +
630u ARG 3.5 8.7 - - - +
631u ALA 3.2 0.2 - - - -
632u PHE* 1.3 78.3 - - - +
634u VAL* 1.3 58.1 + - - +
636u ALA* 3.3 6.6 + - - +
637u SER* 2.9 27.9 + - - -
667u ILE* 4.1 7.5 - - - +
670u GLN* 3.7 30.3 - - + +
671u ILE* 3.7 21.2 - - - +
674u LEU* 5.3 4.9 - - + +
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Residues in contact with VAL 634 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594u ARG* 5.1 23.8 - - + +
597u ILE* 5.4 9.0 - - + -
598u SER* 5.0 6.3 - - - +
630u ARG 2.9 15.8 + - - +
631u ALA* 3.3 4.7 + - - +
633u ALA* 1.3 76.2 - - - +
635u VAL* 1.3 58.1 + - - +
637u SER* 3.3 7.4 + - - +
638u ALA* 2.9 26.7 + - - +
674u LEU* 6.1 1.6 - - - -
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Residues in contact with VAL 635 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597u ILE* 5.4 3.7 - - + +
598u SER* 5.8 0.2 - - - +
601u ALA* 4.0 20.9 - - + -
609u MET* 5.4 10.5 - - + -
631u ALA 3.0 17.5 + - - +
632u PHE* 4.3 3.8 - - - +
634u VAL* 1.3 75.0 - - - +
636u ALA* 1.3 60.2 + - - +
638u ALA* 3.7 7.4 - - - +
639u LEU* 2.9 31.7 + - - +
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Residues in contact with ALA 636 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632u PHE 2.9 19.5 + - - +
633u ALA* 3.6 7.4 - - - +
634u VAL 3.3 0.2 - - - -
635u VAL* 1.3 76.9 - - - +
637u SER* 1.3 59.6 + - - +
639u LEU* 5.4 0.2 - - - -
640u GLY* 2.9 41.7 + - - +
641u ILE* 3.9 5.4 + - - +
644u LEU* 5.8 9.0 - - + -
671u ILE* 5.4 7.6 - - + -
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Residues in contact with SER 637 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633u ALA 2.9 17.3 + - - -
634u VAL* 3.7 7.4 - - - -
636u ALA* 1.3 75.9 - - - +
638u ALA* 1.3 63.2 + - - +
640u GLY* 4.3 2.4 + - - -
671u ILE* 6.5 0.4 - - - -
674u LEU* 5.3 8.3 - - - -
675u MET* 4.8 19.1 - - - -
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Residues in contact with ALA 638 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598u SER* 3.9 34.1 - - - +
601u ALA* 4.6 5.8 - - + -
602u LYS* 5.6 2.0 - - + +
634u VAL 2.9 16.6 + - - +
635u VAL* 3.7 8.3 - - - +
636u ALA 3.2 0.2 - - - -
637u SER* 1.3 80.4 - - - +
639u LEU* 1.3 57.2 + - - +
640u GLY 3.5 0.4 + - - -
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Residues in contact with LEU 639 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601u ALA* 5.9 7.2 - - + +
605u GLY 5.9 2.9 - - - +
606u LEU* 5.7 9.4 - - + -
635u VAL 2.9 15.6 + - - +
636u ALA* 5.4 0.2 - - - -
638u ALA* 1.3 77.3 - - + +
640u GLY* 1.3 64.3 + - - +
643u SER* 3.9 18.1 - - - -
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Residues in contact with GLY 640 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636u ALA* 2.9 25.7 + - - +
637u SER 4.3 2.9 + - - -
638u ALA 3.5 2.8 + - - -
639u LEU* 1.3 83.4 - - - +
641u ILE* 1.3 64.8 + - - +
642u PRO 3.8 0.9 - - - -
643u SER* 4.2 6.7 + - - -
644u LEU* 4.5 3.3 + - - +
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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