Contacts of the helix formed by residues 957 - 967 (chain r) 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 VAL 957 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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897r LEU* 6.1 2.9 - - - +
916r ALA* 4.6 24.5 - - + +
917r VAL* 5.4 0.7 - - - +
920r LEU* 5.8 5.4 - - + -
953r ARG 3.9 7.4 - - - +
954r LEU* 4.5 0.7 - - - +
956r LEU* 1.3 75.0 - - + +
958r HIS* 1.3 57.5 + - - +
959r THR* 3.3 3.7 - - - +
960r ALA* 3.7 18.9 - - + +
961r ALA* 2.9 27.2 + - - +
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Residues in contact with HIS 958 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406r ARG* 4.1 18.2 - - + -
407r GLN 5.0 5.4 - - - +
408r VAL* 6.0 0.9 - - - -
954r LEU 3.3 14.7 + - - +
955r ASP* 3.0 13.6 + - - +
956r LEU 2.9 4.8 + - - -
957r VAL* 1.3 77.2 - - - +
959r THR* 1.3 59.5 + - - +
961r ALA* 3.3 6.9 + - - +
962r LEU* 2.9 27.4 + - - +
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Residues in contact with THR 959 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408r VAL* 5.3 7.5 - - - +
409r LEU* 3.9 30.1 - - - -
411r LEU* 6.0 4.9 - - - -
955r ASP 3.5 7.2 + - - -
956r LEU* 5.8 1.1 - - - -
957r VAL 3.3 2.2 - - - +
958r HIS* 1.3 77.5 - - - +
960r ALA* 1.3 58.9 + - - +
962r LEU* 3.3 7.2 + - - +
963r MET* 2.9 29.3 + - - +
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Residues in contact with ALA 960 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897r LEU* 4.1 10.8 - - + +
898r PRO* 3.7 36.2 - - + +
901r LEU* 4.5 11.2 - - + -
957r VAL* 3.5 20.5 + - - +
958r HIS 3.3 0.4 - - - -
959r THR* 1.3 80.0 - - - +
961r ALA* 1.3 62.3 + - - +
963r MET* 3.2 3.6 + - - +
964r LEU* 2.9 26.3 + - - +
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Residues in contact with ALA 961 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957r VAL 2.9 19.0 + - - +
958r HIS* 3.4 8.7 - - - +
960r ALA* 1.3 76.7 - - - +
962r LEU* 1.3 56.6 + - - +
964r LEU* 3.3 6.1 + - - +
965r ASP* 2.9 29.6 + - - +
970r VAL* 5.3 2.8 - - - +
972r TYR* 5.2 15.5 - - + +
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Residues in contact with LEU 962 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958r HIS 2.9 17.0 + - - +
959r THR* 3.7 8.5 - - - +
961r ALA* 1.3 78.4 - - - +
963r MET* 1.3 56.2 + - - +
965r ASP* 3.2 7.0 + - - +
966r LYS* 2.9 31.8 + - - +
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Residues in contact with MET 963 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898r PRO* 4.5 13.7 - - + -
959r THR 2.9 16.9 + - - +
960r ALA* 3.6 7.4 - - - +
962r LEU* 1.3 75.8 - - - +
964r LEU* 1.3 62.1 + - - +
966r LYS* 3.4 6.1 + - - +
967r ASN* 3.2 24.9 + - - +
995r ASN* 5.5 3.2 - - + +
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Residues in contact with LEU 964 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898r PRO* 5.2 9.6 - - + +
902r ASN* 5.4 7.9 - - + +
960r ALA 2.9 16.6 + - - +
961r ALA* 3.8 5.8 - - - +
963r MET* 1.3 77.8 - - - +
965r ASP* 1.3 60.8 + - - +
967r ASN* 3.7 1.9 + - - -
968r ASN 3.1 2.4 + - - -
969r LEU* 2.8 47.2 + - + -
970r VAL* 3.3 15.5 + - + -
995r ASN* 5.5 6.1 - - + -
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Residues in contact with ASP 965 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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961r ALA 2.9 16.6 + - - +
962r LEU* 3.2 8.3 + - - +
964r LEU* 1.3 76.9 - - - +
966r LYS* 1.3 63.2 + - - +
968r ASN* 3.1 13.7 + - - +
970r VAL* 3.3 18.9 - - - +
971r LYS* 5.5 0.2 - - - -
972r TYR* 4.9 17.0 - - + +
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Residues in contact with LYS 966 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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962r LEU 2.9 17.5 + - - +
963r MET* 3.9 6.3 - - - +
964r LEU 3.4 0.2 - - - -
965r ASP* 1.3 77.6 - - - +
967r ASN* 1.3 59.4 + - - +
968r ASN* 3.3 1.3 + - - +
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Residues in contact with ASN 967 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963r MET 3.2 15.7 + - - +
964r LEU* 4.5 2.0 - - - +
966r LYS* 1.3 77.1 - - - +
968r ASN* 1.3 69.4 + - - +
969r LEU* 3.4 3.9 + - + +
984r LEU* 5.8 1.2 - - - +
995r ASN* 3.4 32.5 - - + +
996r ASP* 5.5 0.7 - - - -
998r VAL* 5.4 1.7 - - - +
999r GLN* 3.7 28.6 + - + +
1002r ASN* 5.6 1.9 - - - +
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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