Contacts of the helix formed by residues 947 - 953 (chain B) in PDB entry 6CNF
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 HIS 947 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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555A GLN* 3.7 14.8 - - + +
556A ASP* 2.5 50.8 + - - -
559A THR* 3.2 27.4 - - + +
710A PHE* 4.9 3.8 - + - -
794A MET* 2.9 32.4 - - - -
799A SER* 4.1 6.8 + - - -
800A LYS* 3.8 28.9 - - + +
761B SER* 3.8 4.4 + - - -
945B ASN* 2.9 25.9 + - - +
946B PRO* 1.3 75.1 - - + +
948B GLY* 1.3 62.2 + - - +
949B PHE 3.2 0.2 - - - -
950B PRO* 3.2 15.5 - - - +
951B SER* 4.0 1.6 + - - -
952B ARG* 4.4 3.1 + - - -
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Residues in contact with GLY 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769B ASP* 4.3 7.4 + - - -
918B GLN* 4.3 11.2 - - - -
944B MET* 5.3 2.0 - - - -
945B ASN* 4.1 9.1 + - - +
946B PRO 2.8 2.6 + - - -
947B HIS* 1.3 79.1 - - - +
949B PHE* 1.3 66.7 + - - +
952B ARG* 3.1 51.1 + - - +
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Residues in contact with PHE 949 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712A ILE* 3.4 27.1 - - + -
809A MET* 3.2 6.6 - - + +
759B VAL* 3.6 31.4 - - + -
918B GLN* 4.3 10.8 - - + -
944B MET* 4.0 21.1 - - + -
945B ASN 5.0 1.3 - - - -
946B PRO 2.9 11.9 + - - +
948B GLY* 1.3 79.7 - - - +
950B PRO* 1.3 58.8 - - + +
953B MET* 2.8 27.2 + - - +
954B THR* 3.5 21.6 + - + +
957B LYS* 3.4 45.3 - - + -
958B MET* 5.4 17.5 - - + -
1018B PHE* 5.8 2.2 - + - -
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Residues in contact with PRO 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712A ILE* 4.9 2.2 - - + -
791A PRO* 5.0 15.9 - - + -
794A MET* 3.4 34.5 - - + -
800A LYS* 4.3 18.8 - - + +
801A GLY* 5.2 0.7 - - - -
805A ASN* 2.2 35.9 + - - +
809A MET* 3.4 10.3 - - + +
946B PRO 3.1 13.9 - - - +
947B HIS* 3.2 12.6 - - - +
949B PHE* 1.3 94.5 - - + +
951B SER* 1.3 53.8 + - - +
953B MET* 3.2 3.8 + - - -
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Residues in contact with SER 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A LYS* 3.0 32.1 - - - +
801A GLY* 2.5 32.7 + - - -
805A ASN* 3.4 8.2 + - - +
695B GLN* 4.0 7.4 + - - +
698B ARG* 5.2 0.2 + - - -
947B HIS 4.0 1.7 + - - -
948B GLY 3.7 1.8 + - - -
949B PHE 3.6 0.2 - - - -
950B PRO* 1.3 75.4 - - - +
952B ARG* 1.3 66.2 + - - +
953B MET* 2.9 10.7 + - - +
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Residues in contact with ARG 952 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511A ASP* 5.1 4.0 - - - +
555A GLN* 5.4 1.6 - - - +
800A LYS* 4.8 14.9 - - - +
695B GLN* 3.1 20.4 + - - +
698B ARG* 3.2 46.4 - - - +
768B GLU* 4.2 14.1 + - - +
769B ASP* 2.3 44.4 + - - -
917B GLY 5.2 1.8 - - - -
918B GLN* 3.4 32.7 + - - +
947B HIS 4.4 3.2 + - - -
948B GLY* 3.1 28.4 + - - +
951B SER* 1.3 75.8 - - - +
953B MET* 1.3 67.4 + - - +
954B THR* 3.3 3.7 + - + -
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Residues in contact with MET 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805A ASN* 3.0 24.7 - - - +
808A GLN* 3.0 32.1 - - - +
809A MET* 3.5 16.8 - - + -
852A PHE* 3.3 37.6 - - + -
864A HIS* 5.1 3.1 - - + -
693B HIS 4.9 0.3 - - - +
694B ASN 4.3 1.4 - - - -
695B GLN* 3.0 45.8 + - + +
949B PHE 2.8 19.8 + - - -
950B PRO 3.3 11.2 - - - +
951B SER 2.9 6.0 - - - +
952B ARG* 1.3 80.9 - - - +
954B THR* 1.3 58.1 + - - +
955B VAL* 4.1 1.7 + - + -
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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