Contacts of the helix formed by residues 644 - 653 (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 LEU 644 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606u LEU* 6.2 3.8 - - + -
636u ALA* 5.8 8.5 - - + -
640u GLY 4.5 3.7 + - - +
641u ILE 3.3 4.8 + - - +
643u SER* 1.3 78.8 - - - +
645u LEU* 1.3 60.2 + - - +
646u PRO* 3.3 2.7 - - - -
647u PHE* 3.1 33.3 + - + +
648u LEU* 3.4 6.1 + - - +
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Residues in contact with LEU 645 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641u ILE* 2.8 21.3 + - + +
642u PRO* 3.7 14.6 - - + +
643u SER 3.7 1.2 - - - -
644u LEU* 1.3 76.5 - - - +
646u PRO* 1.4 56.5 - - - +
648u LEU* 3.2 10.0 + - - +
649u LYS* 3.0 27.5 + - - +
685u SER* 6.1 2.0 - - - +
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Residues in contact with PRO 646 (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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69Y GLU 4.9 0.5 - - - +
70Y PHE* 5.3 7.6 - - - +
73Y ASN* 3.7 29.3 - - + +
74Y GLN* 5.1 3.1 - - + +
642u PRO 5.0 3.0 - - - +
643u SER 5.7 1.8 - - - +
644u LEU* 3.3 2.1 - - - -
645u LEU* 1.4 75.5 - - - +
647u PHE* 1.3 57.5 + - - +
649u LYS* 3.7 8.5 - - + +
650u ALA* 2.9 30.0 + - - +
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Residues in contact with PHE 647 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610u ILE* 5.6 10.3 - - + -
644u LEU* 3.1 24.7 + - + +
646u PRO* 1.3 77.9 - - - +
648u LEU* 1.3 58.4 + - - +
650u ALA* 3.3 6.1 + - - +
651u VAL* 2.9 31.9 + - - +
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Residues in contact with LEU 648 (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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644u LEU 3.4 6.2 + - - +
645u LEU* 3.2 11.7 + - - +
647u PHE* 1.3 77.4 - - - +
649u LYS* 1.3 58.9 + - - +
651u VAL* 3.4 3.0 + - - +
652u CYS* 3.0 34.7 + - - +
664u GLY* 5.3 12.6 - - - +
667u ILE* 5.7 6.7 - - + -
668u VAL* 6.3 1.6 - - + +
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Residues in contact with LYS 649 (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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69Y GLU* 5.1 1.3 - - - +
73Y ASN* 5.0 9.4 - - + -
645u LEU 3.0 16.6 + - - +
646u PRO* 3.9 8.5 - - + +
648u LEU* 1.3 77.7 - - - +
650u ALA* 1.3 61.3 + - - +
652u CYS* 4.6 2.9 - - - +
653u LYS* 3.8 19.8 + - - +
689u ILE* 5.5 11.0 - - + -
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Residues in contact with ALA 650 (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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65Y ASP 5.1 0.2 - - - +
66Y VAL* 3.7 24.3 - - + +
69Y GLU* 3.7 35.5 + - + +
70Y PHE* 4.4 2.0 - - + +
646u PRO 2.9 19.1 + - - +
647u PHE* 3.5 7.6 - - - +
648u LEU 3.2 0.2 - - - -
649u LYS* 1.3 76.3 - - - +
651u VAL* 1.3 65.2 + - - +
652u CYS 3.4 0.7 + - - -
653u LYS 3.5 10.0 + - - -
654u SER* 3.7 13.3 + - - -
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Residues in contact with VAL 651 (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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66Y VAL* 5.6 7.0 - - + -
647u PHE 2.9 17.2 + - - +
648u LEU* 3.4 4.0 + - - +
650u ALA* 1.3 76.3 - - - +
652u CYS* 1.3 60.2 + - - +
653u LYS 3.6 0.3 + - - -
654u SER* 4.1 8.5 + - - +
660u ALA* 3.4 38.7 - - + +
661u ARG* 3.7 1.6 + - - -
663u THR* 6.4 0.4 - - - -
664u GLY* 4.9 8.1 - - - -
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Residues in contact with CYS 652 (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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648u LEU 3.0 18.2 + - - +
649u LYS* 4.7 3.8 - - - +
650u ALA 3.3 0.2 - - - -
651u VAL* 1.3 79.4 - - - +
653u LYS* 1.3 57.5 + - + +
654u SER 3.6 1.4 - - - +
660u ALA 5.0 0.4 - - - -
661u ARG* 4.0 25.1 - - + +
664u GLY* 5.1 12.5 - - - -
665u ILE* 5.2 2.2 - - + +
689u ILE* 5.1 14.6 - - + +
692u HIS* 5.8 3.5 - - - +
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Residues in contact with LYS 653 (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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69Y GLU* 6.5 0.9 - - + -
649u LYS 3.8 14.4 + - - +
650u ALA 3.5 5.5 + - - +
651u VAL 3.4 0.6 - - - -
652u CYS* 1.3 77.9 - - + +
654u SER* 1.3 61.6 + - - +
655u LYS* 4.0 1.7 + - - +
692u HIS* 5.8 7.9 - - + -
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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