Contacts of the helix formed by residues 939 - 952 (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 GLN 939 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99M HIS* 3.2 17.1 - - - +
100M GLU* 4.9 0.2 - - - -
102M ALA* 3.7 3.6 - - - +
103M PHE 1.8 37.2 - - - +
104M VAL* 1.8 42.8 + - - +
105M PHE 3.2 0.2 - - - +
935U PHE 2.8 9.1 + - - -
938U TYR* 1.3 74.1 - - - +
940U VAL* 1.3 59.9 + - - +
943U ARG* 3.5 15.8 + - - +
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Residues in contact with VAL 940 (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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104M VAL* 4.9 1.6 - - - +
935U PHE 3.3 1.5 + - - +
936U PHE* 3.1 24.0 + - + +
939U GLN* 1.3 78.7 - - - +
941U MET* 1.3 65.6 + - - +
942U SER 3.2 0.7 - - - -
943U ARG* 3.3 5.6 + - - +
944U TRP* 3.0 23.9 + - - +
1001U ILE* 6.3 2.9 - - + -
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Residues in contact with MET 941 (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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131M ARG 4.9 0.4 - - - +
134M ASP* 3.4 9.6 - - + +
135M ARG* 2.5 49.4 - - + +
936U PHE 2.7 13.8 + - - +
940U VAL* 1.3 73.2 - - - +
942U SER* 1.3 56.2 + - - +
944U TRP* 3.3 6.2 + - - +
945U GLU* 2.8 33.6 + - - +
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Residues in contact with SER 942 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95M VAL* 3.2 11.6 - - - +
96M ASN* 3.5 9.7 - - - -
99M HIS* 1.0 63.0 - - - -
135M ARG* 4.1 4.2 - - - +
937U LEU 3.8 6.7 + - - -
938U TYR* 3.6 7.0 - - - -
940U VAL 3.2 0.8 - - - -
941U MET* 1.3 78.1 - - - +
943U ARG* 1.3 59.0 + - - +
945U GLU* 3.8 5.5 - - - +
946U GLU 3.0 19.2 + - - -
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Residues in contact with ARG 943 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96M ASN 4.7 4.5 - - - -
99M HIS* 3.1 2.9 - - - +
100M GLU* 4.8 13.7 - - + +
939U GLN 3.5 17.6 + - - +
940U VAL* 3.3 5.7 + - - +
942U SER* 1.3 78.8 - - - +
944U TRP* 1.3 62.4 + - - +
946U GLU* 3.6 6.3 + - - +
947U TYR* 3.1 23.4 + - - +
969U PRO* 4.1 23.6 - - + +
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Residues in contact with TRP 944 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940U VAL 3.0 17.2 + - - +
941U MET* 3.7 7.0 - - - +
942U SER 3.2 0.2 - - - -
943U ARG* 1.3 75.4 - - - +
945U GLU* 1.3 60.3 + - - +
947U TYR* 3.1 7.5 + - - +
948U ILE* 2.8 30.6 + - - +
969U PRO* 5.3 1.8 - - - +
998U PHE* 5.6 10.5 - - + -
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Residues in contact with GLU 945 (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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92M TYR* 4.6 4.4 - - - +
95M VAL* 5.6 8.5 - - + -
131M ARG* 5.1 16.4 - - + +
135M ARG* 6.1 1.3 - - + -
941U MET 2.8 21.5 + - - +
942U SER* 3.8 5.4 - - - +
944U TRP* 1.3 73.9 - - - +
946U GLU* 1.3 57.5 + - - +
948U ILE* 3.9 5.7 - - - +
949U SER* 3.0 29.5 + - - -
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Residues in contact with GLU 946 (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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92M TYR 3.8 7.8 + - - -
96M ASN* 1.8 49.1 - - + +
942U SER 3.0 8.3 + - - +
943U ARG* 3.8 5.6 - - - +
945U GLU* 1.3 77.5 - - - +
947U TYR* 1.3 62.3 + - - +
949U SER* 3.3 6.4 + - - -
950U LYS* 3.2 21.1 + - - +
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Residues in contact with TYR 947 (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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943U ARG 3.1 16.0 + - - +
944U TRP* 3.1 11.6 + - - +
946U GLU* 1.3 74.7 - - - +
948U ILE* 1.3 65.4 + - - +
950U LYS* 3.0 16.3 + - - +
951U VAL* 3.0 17.3 + - - +
967U PHE* 4.2 22.9 - - + +
968U PHE* 5.6 1.6 - - - -
969U PRO* 5.0 7.2 - - + -
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Residues in contact with ILE 948 (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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944U TRP 2.8 19.4 + - - +
945U GLU* 3.9 6.5 - - - +
947U TYR* 1.3 72.0 - - - +
949U SER* 1.3 57.4 + - - +
951U VAL* 5.2 0.9 - - - -
952U LYS* 2.8 47.8 + - + +
953U ASN* 4.4 0.2 - - - +
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Residues in contact with SER 949 (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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89M ASP* 6.2 0.2 - - - -
92M TYR* 3.2 36.1 - - - -
945U GLU 3.0 15.4 + - - -
946U GLU 3.3 7.6 - - - -
948U ILE* 1.3 76.1 - - - +
950U LYS* 1.3 59.3 + - - +
953U ASN* 3.5 25.3 - - - +
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Residues in contact with LYS 950 (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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946U GLU 3.2 9.5 + - - +
947U TYR* 3.0 10.8 + - - +
949U SER* 1.3 79.8 - - - +
951U VAL* 1.3 61.1 + - + +
952U LYS 3.5 0.4 + - - -
953U ASN 4.3 8.7 - - - +
959U PRO* 5.9 1.9 - - - +
967U PHE* 5.1 12.6 - - + -
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Residues in contact with VAL 951 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947U TYR 3.0 12.7 + - - +
948U ILE* 5.4 0.7 - - - -
950U LYS* 1.3 78.2 - - + +
952U LYS* 1.3 61.2 + - - +
953U ASN 3.7 1.6 - - - -
959U PRO* 5.1 16.6 - - + +
960U ASP 6.0 0.7 - - - +
963U GLU* 4.5 22.7 - - + +
964U VAL* 4.8 10.8 - - + +
967U PHE* 5.9 1.8 - - + -
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Residues in contact with LYS 952 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948U ILE* 2.8 26.0 + - + +
951U VAL* 1.3 80.1 - - - +
953U ASN* 1.3 63.3 + - - +
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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
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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