Contacts of the helix formed by residues 895 - 900 (chain D) in PDB entry 7C17
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 CYS 895 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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809D VAL* 4.0 5.1 - - - +
811D GLU* 3.4 31.0 - - - -
812D ASP 3.4 14.1 - - - +
813D ASP* 3.7 2.9 - - - +
814D CYS* 3.5 18.8 - - - -
888D CYS* 3.6 3.0 - - - -
890D THR* 3.9 11.9 - - - -
894D VAL* 1.3 81.1 - - - +
896D ALA* 1.3 64.4 + - - +
897D HIS 3.5 0.4 - - - -
898D CYS* 3.8 4.9 - - - +
899D TYR* 3.6 21.8 + - - +
1502D ZN 2.5 32.3 - - - -
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Residues in contact with ALA 896 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809D VAL* 3.7 14.6 - - + +
811D GLU 3.1 7.3 + - - +
812D ASP* 2.9 17.1 + - + +
895D CYS* 1.3 72.7 - - - +
897D HIS* 1.3 68.3 + - + +
898D CYS 3.2 4.9 + - - -
900D GLY 3.5 16.3 + - - +
908D ILE* 4.9 3.0 - - + +
909D ILE* 3.4 47.4 - - + +
910D ASN 5.4 0.4 - - - -
911D LYS* 5.6 1.1 - - + +
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Residues in contact with HIS 897 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812D ASP* 2.6 43.2 + - + +
813D ASP* 3.6 21.8 - - + +
843D VAL* 3.4 28.1 - - + +
861D ASN* 4.4 26.0 - - + +
862D THR* 6.0 0.2 - - - -
863D LEU* 5.9 7.0 - - + -
883D ARG* 3.5 11.6 + - - -
896D ALA* 1.3 74.1 - - + +
898D CYS* 1.3 59.2 + - - +
899D TYR 3.7 0.2 - - - -
900D GLY 5.5 0.2 - - - -
908D ILE* 4.1 32.4 - - + +
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Residues in contact with CYS 898 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813D ASP* 3.5 18.4 - - - -
814D CYS* 3.8 7.4 - - - -
816D THR* 4.4 4.7 - - - -
843D VAL* 3.7 2.5 - - - -
883D ARG* 3.3 30.6 - - - +
884D SER 3.0 35.1 - - - +
885D VAL* 4.6 0.7 - - - -
888D CYS* 4.1 8.1 - - + -
894D VAL* 5.2 1.6 - - + -
895D CYS* 3.7 8.0 + - + +
896D ALA 3.2 1.0 - - - -
897D HIS* 1.3 78.1 - - - +
899D TYR* 1.3 59.7 + - - +
1502D ZN 2.5 36.6 - - - -
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Residues in contact with TYR 899 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842D ARG* 4.5 1.6 + - - +
843D VAL* 3.8 6.9 + - - +
883D ARG 4.6 3.5 - - - +
884D SER* 5.6 0.8 - - - +
885D VAL* 3.8 22.0 - - + -
894D VAL* 4.6 0.2 - - + -
895D CYS 3.6 12.2 + - - +
896D ALA 3.7 1.1 + - - +
898D CYS* 1.3 80.4 - - - +
900D GLY* 1.3 62.1 + - - +
901D ARG 3.6 19.3 + - - -
902D ASP* 4.5 1.5 - - - -
903D LEU* 5.2 2.8 + - - +
909D ILE* 3.6 31.0 - - + -
915D ILE* 3.6 43.4 - - + +
918D ILE* 5.1 2.4 - - - +
1251D LYS* 3.5 57.3 + - + +
1252D HIS* 3.4 26.5 - - - -
1254D GLU* 5.6 0.7 - - - -
1255D VAL* 5.8 0.9 - - + -
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Residues in contact with GLY 900 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841D GLY 3.4 11.9 - - - -
843D VAL* 3.7 21.8 - - - +
863D LEU* 3.4 14.4 - - - +
896D ALA 3.5 9.1 + - - +
899D TYR* 1.3 82.9 - - - +
901D ARG* 1.3 60.3 + - - -
908D ILE* 4.9 0.9 - - - +
909D ILE* 3.5 19.9 + - - +
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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