Contacts of the helix formed by residues 995 - 1007 (chain F) in PDB entry 6C3P
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 ILE 995 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994F GLU* 1.3 78.2 - - + +
996F PRO* 1.3 69.9 - - + +
998F ARG* 3.2 6.7 + - - +
999F ALA* 2.9 26.1 + - - +
1305F GLU* 5.9 0.2 - - - +
1312F LYS* 5.1 18.0 - - + +
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Residues in contact with PRO 996 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994F GLU* 3.6 11.2 - - + +
995F ILE* 1.3 92.9 - - + +
997F TRP* 1.3 64.3 + - - +
999F ALA* 4.0 4.6 - - + +
1000F CYS* 2.9 28.2 + - - +
1182F ARG* 5.1 6.1 - - - +
1186F ARG* 5.4 7.9 - - - +
1305F GLU* 3.3 36.3 - - - +
1308F LEU* 5.4 4.9 - - + +
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Residues in contact with TRP 997 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994F GLU 3.3 22.2 + - - +
996F PRO* 1.3 80.7 - - - +
998F ARG* 1.3 58.1 + - - +
1000F CYS* 4.0 2.9 - - - +
1001F ALA* 2.9 31.9 + - - +
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Residues in contact with ARG 998 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994F GLU 3.0 15.6 + - - +
995F ILE* 3.7 6.3 - - - +
997F TRP* 1.3 76.1 - - - +
999F ALA* 1.3 57.9 + - - +
1001F ALA* 3.2 6.4 + - - +
1002F LYS* 2.9 30.0 + - - +
1312F LYS* 6.5 0.2 - - + -
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Residues in contact with ALA 999 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995F ILE 2.9 16.9 + - - +
996F PRO* 4.0 4.3 - - + +
998F ARG* 1.3 77.2 - - - +
1000F CYS* 1.3 58.1 + - - +
1002F LYS* 3.3 5.9 + - - +
1003F TYR* 3.0 26.2 + - - +
1308F LEU* 3.7 31.9 - - + +
1311F VAL* 4.8 3.6 - - - +
1312F LYS* 3.9 27.7 - - + +
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Residues in contact with CYS1000 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996F PRO 2.9 17.9 + - - +
997F TRP* 4.1 2.9 - - - +
999F ALA* 1.3 76.5 - - - +
1001F ALA* 1.3 58.0 + - - +
1003F TYR* 3.3 7.0 + - - +
1004F LEU* 2.9 43.0 + - - +
1139F LEU* 5.9 0.9 - - - -
1304F MET* 3.9 26.0 - - + -
1308F LEU* 3.5 20.1 - - + +
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Residues in contact with ALA1001 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997F TRP 2.9 20.8 + - - +
998F ARG* 3.5 7.0 - - - +
999F ALA 3.2 0.2 - - - -
1000F CYS* 1.3 77.7 - - - +
1002F LYS* 1.3 58.3 + - - +
1004F LEU* 3.2 19.2 - - + +
1005F SER* 2.8 29.3 + - - -
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Residues in contact with LYS1002 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998F ARG 2.9 16.4 + - - +
999F ALA* 3.8 5.4 - - - +
1001F ALA* 1.3 73.2 - - - +
1003F TYR* 1.3 66.3 + - - +
1005F SER* 3.1 9.3 + - - -
1006F SER* 3.0 25.6 + - - -
1311F VAL* 6.3 0.9 - - + -
1315F HIS* 4.8 27.8 - - + +
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Residues in contact with TYR1003 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999F ALA 3.0 14.6 + - - +
1000F CYS* 3.3 13.9 - - - +
1002F LYS* 1.3 75.5 - - - +
1004F LEU* 1.3 67.7 + - + +
1006F SER* 3.1 24.2 + - - -
1088F THR* 5.8 2.5 - - + -
1089F GLY* 4.0 22.5 + - - -
1092F VAL* 3.3 41.7 - - + +
1096F LEU* 4.4 2.2 - - + -
1131F ILE* 4.4 11.4 - - + +
1135F ILE* 3.0 47.5 - - + +
1136F PRO* 5.0 0.2 - - - +
1139F LEU* 5.0 14.1 - - + +
1304F MET* 6.1 2.2 - - + -
1308F LEU* 3.8 17.0 - - + -
1311F VAL* 3.9 27.7 - - + +
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Residues in contact with LEU1004 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000F CYS* 2.9 36.1 + - - +
1001F ALA* 3.2 26.2 - - + +
1003F TYR* 1.3 81.8 - - + +
1005F SER* 1.3 57.8 + - - +
1007F ALA* 2.7 41.2 + - + +
1012F LEU* 3.5 48.5 - - + +
1092F VAL* 5.0 0.4 - - - -
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Residues in contact with SER1005 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001F ALA 2.8 19.3 + - - -
1002F LYS* 3.1 12.5 + - - -
1004F LEU* 1.3 78.9 - - - +
1006F SER* 1.3 65.8 + - - +
1007F ALA 2.9 9.6 - - - +
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Residues in contact with SER1006 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002F LYS 3.0 14.0 + - - -
1003F TYR* 3.1 12.7 + - - -
1005F SER* 1.3 77.3 - - - +
1007F ALA* 1.3 54.6 + - - +
1008F GLY 4.2 0.2 + - - -
1091F LYS* 4.8 2.9 - - - +
1092F VAL* 3.6 27.1 - - - +
1095F ARG* 4.3 21.2 - - - +
1096F LEU* 3.9 17.5 - - - +
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Residues in contact with ALA1007 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003F TYR 3.7 0.4 + - - -
1004F LEU* 2.7 28.4 + - - +
1005F SER* 2.9 11.9 - - - +
1006F SER* 1.3 80.0 - - - +
1008F GLY* 1.3 68.1 + - - +
1009F ILE* 3.6 1.6 + - - -
1011F LEU* 3.6 13.0 - - + -
1012F LEU* 4.5 2.2 - - + +
1088F THR* 3.3 26.9 - - - +
1091F LYS* 5.3 3.1 - - - +
1092F VAL* 3.5 16.1 - - + +
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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