Contacts of the helix formed by residues 986 - 1004 (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 TYR 986 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1506A ALA* 4.8 9.7 - - + +
1507A SER* 5.8 1.3 - - - +
984u GLU* 3.6 5.8 - - + +
985u GLU* 1.3 77.7 - - - +
987u PRO* 1.3 59.5 - - - +
988u GLU* 4.4 3.4 - - + +
989u VAL* 4.0 20.6 - - + +
990u LEU* 3.1 26.0 + - - +
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Residues in contact with PRO 987 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985u GLU 3.6 5.0 - - - +
986u TYR* 1.3 71.0 - - - +
988u GLU* 1.3 60.7 + - - +
990u LEU* 3.8 6.6 - - + +
991u GLY* 2.9 26.9 + - - -
1028u HIS* 3.7 30.1 - - + -
1030u LYS* 5.4 2.6 - - - +
1031u VAL* 4.8 8.6 + - + +
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Residues in contact with GLU 988 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949u GLN* 3.4 19.0 - - + +
986u TYR* 3.3 3.2 - - + +
987u PRO* 1.3 77.9 - - - +
989u VAL* 1.3 59.8 + - - +
991u GLY* 4.7 0.6 - - - -
992u SER* 3.9 8.5 + - - -
1030u LYS* 6.2 2.5 - - - -
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Residues in contact with VAL 989 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948u ARG* 4.6 21.1 - - + -
949u GLN* 4.2 10.6 - - + +
952u ALA* 5.0 1.0 - - - +
984u GLU* 4.9 7.6 - - + -
986u TYR* 3.6 20.8 + - + +
987u PRO 3.2 0.2 - - - -
988u GLU* 1.3 78.2 - - - +
990u LEU* 1.3 60.6 + - - +
991u GLY 3.3 0.2 - - - -
992u SER* 3.2 5.2 + - - -
993u ILE* 2.9 27.3 + - - +
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Residues in contact with LEU 990 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982u LEU* 5.5 9.6 - - + +
984u GLU* 4.4 16.1 - - + +
986u TYR 3.1 18.3 + - - +
987u PRO* 3.3 7.8 + - + +
989u VAL* 1.3 77.2 - - - +
991u GLY* 1.3 57.0 + - - +
993u ILE* 3.3 9.1 + - - +
994u LEU* 2.9 29.8 + - - +
1031u VAL* 5.3 8.3 - - + -
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Residues in contact with GLY 991 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
987u PRO 2.9 16.6 + - - -
988u GLU* 4.7 1.6 - - - -
990u LEU* 1.3 77.6 - - - +
992u SER* 1.3 56.3 + - - +
994u LEU* 3.4 5.2 + - - +
995u GLY* 2.9 23.9 + - - -
1030u LYS* 4.6 10.3 - - - -
1031u VAL* 4.5 21.2 - - - +
1034u ASN* 4.1 5.0 - - - +
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Residues in contact with SER 992 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949u GLN* 3.5 39.0 - - - -
952u ALA* 3.4 17.8 - - - +
953u ASP* 4.3 7.7 - - - +
988u GLU 3.9 4.1 + - - -
989u VAL 3.2 8.9 + - - -
991u GLY* 1.3 72.8 - - - +
993u ILE* 1.3 59.7 + - - +
995u GLY* 3.8 2.0 - - - +
996u ALA* 2.9 24.1 + - - +
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Residues in contact with ILE 993 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952u ALA* 3.8 10.7 - - + +
978u LEU* 5.1 10.5 - - + +
981u TYR* 4.3 20.2 - - + +
982u LEU* 4.8 12.1 - - + -
989u VAL 2.9 13.8 + - - +
990u LEU* 3.6 12.8 - - - +
991u GLY 3.3 0.2 - - - -
992u SER* 1.3 76.1 - - - +
994u LEU* 1.3 57.2 + - - +
996u ALA* 3.3 4.5 + - - +
997u LEU* 3.0 28.8 + - - +
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Residues in contact with LEU 994 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982u LEU* 5.9 0.6 - - - +
990u LEU 2.9 17.1 + - - +
991u GLY* 3.8 2.0 - - - +
993u ILE* 1.3 75.9 - - - +
995u GLY* 1.3 56.8 + - - +
997u LEU* 3.8 6.7 - - - +
998u LYS* 2.8 28.8 + - - +
1031u VAL* 5.3 2.9 - - - +
1034u ASN* 3.7 29.6 - - + +
1035u CYS* 4.7 4.7 - - + +
1038u LEU* 5.4 3.9 - - + +
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Residues in contact with GLY 995 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956u SER* 3.9 7.6 - - - -
991u GLY 2.9 17.1 + - - -
992u SER* 3.3 2.9 + - - -
993u ILE 3.3 0.2 - - - -
994u LEU* 1.3 75.2 - - - +
996u ALA* 1.3 60.3 + - - +
998u LYS* 3.3 8.9 + - - +
999u ALA* 2.9 27.9 + - - +
1034u ASN* 4.2 6.0 - - - +
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Residues in contact with ALA 996 (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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952u ALA* 3.3 27.8 - - + +
955u ILE* 4.2 14.9 - - + +
956u SER* 3.8 12.3 - - - +
959u ALA* 5.5 0.7 - - - +
978u LEU* 5.5 7.9 - - + -
992u SER 2.9 13.7 + - - +
993u ILE* 3.6 6.3 - - - +
995u GLY* 1.3 76.0 - - - +
997u LEU* 1.3 56.8 + - - +
999u ALA* 3.2 4.0 + - - +
1000u ILE* 2.9 26.6 + - - +
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Residues in contact with LEU 997 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978u LEU* 5.1 19.9 - - + +
993u ILE 3.0 16.5 + - - +
994u LEU* 3.9 7.0 - - - +
996u ALA* 1.3 72.7 - - - +
998u LYS* 1.3 59.0 + - - +
1000u ILE* 3.3 9.2 + - - +
1001u VAL* 3.0 29.6 + - - +
1038u LEU* 6.1 0.7 - - - -
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Residues in contact with LYS 998 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994u LEU 2.8 18.7 + - - +
995u GLY* 3.3 10.5 - - - +
997u LEU* 1.3 76.0 - - - +
999u ALA* 1.3 57.3 + - - +
1001u VAL* 3.3 7.2 + - - +
1002u ASN* 2.9 28.6 + - - +
1034u ASN* 5.3 5.4 - - + +
1037u ASP* 6.1 2.9 - - + -
1038u LEU* 5.0 18.1 - - + +
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Residues in contact with ALA 999 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956u SER* 3.7 30.3 - - - +
959u ALA* 3.8 12.7 - - + +
995u GLY 2.9 14.0 + - - +
996u ALA 3.6 7.4 - - - +
998u LYS* 1.3 72.7 - - - +
1000u ILE* 1.3 61.5 + - - +
1002u ASN* 3.7 7.6 - - - +
1003u VAL* 3.0 32.4 + - - +
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Residues in contact with ILE1000 (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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959u ALA* 4.5 6.8 - - + +
975u GLY* 6.0 6.5 - - - -
996u ALA 2.9 13.3 + - - +
997u LEU* 3.5 12.8 - - - +
999u ALA* 1.3 77.2 - - - +
1001u VAL* 1.3 57.2 + - - +
1003u VAL* 4.6 1.0 - - - +
1004u ILE* 3.0 36.8 + - + +
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Residues in contact with VAL1001 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997u LEU 3.0 17.4 + - - +
998u LYS* 3.7 6.7 - - - +
1000u ILE* 1.3 75.2 - - - +
1002u ASN* 1.3 58.6 + - - +
1004u ILE 2.9 20.0 - - - +
1006u MET* 5.1 9.8 + - + +
1038u LEU* 6.4 2.2 - - + -
1041u ARG* 5.7 9.0 - - + -
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Residues in contact with ASN1002 (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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998u LYS 2.9 17.1 + - - +
999u ALA* 3.7 8.7 - - - +
1000u ILE 3.2 0.4 - - - -
1001u VAL* 1.3 79.3 - - - +
1003u VAL* 1.3 62.9 + - + +
1004u ILE 3.5 2.1 + - - +
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Residues in contact with VAL1003 (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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959u ALA* 3.7 27.6 - - + +
960u VAL* 4.7 6.7 - - + -
963u LYS* 4.6 18.4 - - + +
999u ALA 3.0 17.3 + - - +
1000u ILE* 4.6 1.3 - - - +
1002u ASN* 1.3 77.1 - - + +
1004u ILE* 1.3 60.4 + - - +
1005u GLY 4.2 0.5 + - - -
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Residues in contact with ILE1004 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971u MET* 6.1 5.4 - - + -
1000u ILE* 3.0 15.3 + - + +
1001u VAL* 2.9 22.6 - - - +
1002u ASN 4.0 2.1 - - - +
1003u VAL* 1.3 77.5 - - + +
1005u GLY* 1.3 71.1 + - - +
1006u MET* 3.5 0.9 + - - -
1008u LYS 5.5 3.1 - - - +
1009u MET* 5.4 9.0 - - + -
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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