Contacts of the helix formed by residues 884 - 893 (chain G) in PDB entry 6V3O
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 ASP 884 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135G GLY 4.7 3.6 - - - +
136G SER* 3.7 30.4 + - - -
651G PRO* 6.0 1.0 - - - +
881G LEU* 3.0 28.5 + - + +
883G GLY* 1.3 79.5 - - - +
885G PRO* 1.3 67.0 - - - +
886G PHE* 3.7 6.6 + - - +
887G LEU* 3.1 35.4 + - - +
888G LYS* 3.0 21.1 + - - +
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Residues in contact with PRO 885 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G VAL* 3.6 26.1 - - + +
881G LEU 4.0 1.5 - - - +
882G GLU 4.4 8.7 - - - +
883G GLY 3.6 7.6 - - - +
884G ASP* 1.3 89.1 - - - +
886G PHE* 1.3 66.5 + - + +
888G LYS* 3.7 10.3 - - + +
889G GLN* 2.8 31.2 + - - +
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Residues in contact with PHE 886 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G VAL* 3.8 40.8 - - + -
29G SER* 4.3 12.3 - - - -
32G ASP* 6.3 0.9 - - + -
113G GLU* 5.5 0.3 - - - +
116G GLN* 5.4 2.0 - - - -
120G ARG* 3.9 33.9 - - - +
126G LEU* 4.0 31.4 - - + -
136G SER* 5.1 1.1 - - - +
138G THR* 3.5 36.1 - - + -
884G ASP* 3.2 6.9 - - - +
885G PRO* 1.3 87.9 - - + +
887G LEU* 1.3 62.4 + - - +
889G GLN* 3.4 13.7 + - - +
890G GLY* 3.1 19.2 + - - -
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Residues in contact with LEU 887 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G GLU* 5.8 3.8 - - - +
647G ARG* 4.2 12.6 - - - +
651G PRO* 6.1 1.6 - - + -
831G MET* 4.2 16.2 - - + -
881G LEU* 3.7 29.8 - - + -
884G ASP* 3.1 34.0 + - - +
886G PHE* 1.3 73.5 - - - +
888G LYS* 1.3 66.3 + - - +
890G GLY* 3.3 2.2 + - - -
891G LEU* 3.1 51.4 + - + +
894G ARG* 5.9 0.7 - - - +
1001G GOL 4.1 23.6 - - - +
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Residues in contact with LYS 888 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G PRO* 6.3 4.3 - - + -
834G ALA* 6.1 1.6 - - + -
879G ASP* 3.7 17.4 + - - +
880G ILE* 2.7 46.4 + - + +
881G LEU* 4.2 21.7 - - + +
882G GLU* 5.9 0.9 - - - -
884G ASP 3.0 17.8 + - - +
885G PRO* 3.7 9.6 - - + +
887G LEU* 1.3 76.2 - - - +
889G GLN* 1.3 62.2 + - - +
891G LEU* 3.6 3.9 + - - +
892G VAL* 3.1 29.6 + - + +
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Residues in contact with GLN 889 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G VAL* 3.7 25.5 - - + +
26G GLY 3.9 7.1 - - - +
28G VAL* 3.1 22.9 - - + +
32G ASP* 2.8 37.5 + - - +
34G LEU* 4.1 16.4 - - + +
116G GLN* 4.2 6.9 + - - +
885G PRO 2.8 18.3 + - - +
886G PHE* 3.6 11.7 + - - +
888G LYS* 1.3 74.2 - - - +
890G GLY* 1.3 64.4 + - - +
892G VAL* 3.3 11.5 - - - +
893G LEU* 3.1 37.6 - - + +
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Residues in contact with GLY 890 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G LEU* 4.6 11.2 - - - -
113G GLU* 3.8 26.2 - - - +
886G PHE 3.1 14.8 + - - -
887G LEU* 3.3 3.5 + - - -
889G GLN* 1.3 77.4 - - - +
891G LEU* 1.3 62.8 + - - +
893G LEU* 3.8 6.4 + - - +
894G ARG* 3.5 24.5 + - - +
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Residues in contact with LEU 891 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G GLU* 5.7 0.2 - - - +
831G MET* 4.4 4.5 - - + +
834G ALA* 4.1 23.6 - - + +
835G LYS* 3.7 39.5 - - + -
881G LEU* 4.3 3.8 - - + -
887G LEU* 3.1 41.7 + - + +
888G LYS* 4.2 3.6 - - - +
890G GLY* 1.3 75.3 - - - +
892G VAL* 1.3 64.4 + - - +
894G ARG* 3.0 54.1 + - - +
895G ASN* 3.6 13.0 + - - +
1001G GOL 3.9 6.1 - - - +
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Residues in contact with VAL 892 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G LEU* 3.8 44.2 - - + +
24G VAL* 4.9 4.9 - - + -
72G GLU* 5.2 1.8 - - + +
888G LYS* 3.1 23.1 + - + +
889G GLN* 3.3 14.4 - - - +
891G LEU* 1.3 79.5 - - - +
893G LEU* 1.3 73.6 + - + +
895G ASN* 3.2 27.3 + - - +
896G PRO* 3.4 9.9 - - - +
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Residues in contact with LEU 893 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G LEU* 4.1 38.9 - - + +
23G LEU* 4.9 4.9 - - + -
24G VAL* 4.8 12.3 - - + -
34G LEU* 3.6 35.9 - - + -
35G ILE* 4.9 9.9 - - + +
38G ASP* 3.9 20.5 - - - +
109G ALA* 4.9 2.4 - - + +
889G GLN* 3.1 26.9 + - + +
890G GLY* 4.2 4.3 - - - +
891G LEU 3.2 1.0 - - - -
892G VAL* 1.3 86.1 - - + +
894G ARG* 1.3 59.9 + - + +
896G PRO* 3.8 7.4 - - - +
897G TYR* 3.4 20.3 - - - -
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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