Contacts of the helix formed by residues 995 - 1007 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994G GLU* 1.3 79.7 - - + +
996G PRO* 1.3 69.6 - - + +
998G ARG* 3.2 6.9 + - - +
999G ALA* 2.9 25.2 + - - +
1305G GLU* 5.9 0.2 - - - +
1312G LYS* 5.1 18.2 - - + +
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Residues in contact with PRO 996 (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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994G GLU* 3.6 11.7 - - + +
995G ILE* 1.3 93.4 - - + +
997G TRP* 1.3 63.9 + - - +
999G ALA* 4.0 4.6 - - + +
1000G CYS* 2.9 28.1 + - - +
1182G ARG* 5.1 6.7 - - - +
1186G ARG* 5.4 7.2 - - - +
1305G GLU* 3.3 35.9 - - - +
1308G LEU* 5.4 4.4 - - + +
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Residues in contact with TRP 997 (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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994G GLU* 3.3 20.5 + - - +
996G PRO* 1.3 80.3 - - - +
998G ARG* 1.3 57.2 + - - +
1000G CYS* 3.8 3.2 - - - +
1001G ALA* 2.9 31.7 + - - +
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Residues in contact with ARG 998 (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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994G GLU 3.0 16.1 + - - +
995G ILE* 3.7 6.1 - - - +
997G TRP* 1.3 76.4 - - - +
999G ALA* 1.3 58.2 + - - +
1001G ALA* 3.2 6.7 + - - +
1002G LYS* 2.9 30.0 + - - +
1312G LYS* 6.5 0.7 - - + -
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Residues in contact with ALA 999 (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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995G ILE 2.9 16.9 + - - +
996G PRO* 4.0 4.3 - - + +
998G ARG* 1.3 77.9 - - - +
1000G CYS* 1.3 57.1 + - - +
1002G LYS* 3.3 5.7 + - - +
1003G TYR* 3.0 26.7 + - - +
1308G LEU* 3.7 31.9 - - + +
1309G GLY* 5.6 0.2 - - - -
1311G VAL* 4.8 3.3 - - - +
1312G LYS* 3.9 26.2 - - + +
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Residues in contact with CYS1000 (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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996G PRO 2.9 18.3 + - - +
997G TRP* 4.1 2.5 - - - +
999G ALA* 1.3 75.4 - - - +
1001G ALA* 1.3 57.7 + - - +
1003G TYR* 3.3 6.0 + - - +
1004G LEU* 2.9 43.2 + - - +
1139G LEU* 5.9 1.1 - - - -
1304G MET* 3.9 25.1 - - + -
1308G LEU* 3.5 21.0 - - + +
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Residues in contact with ALA1001 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997G TRP 2.9 20.8 + - - +
998G ARG* 3.5 8.1 - - - +
999G ALA 3.2 0.2 - - - -
1000G CYS* 1.3 76.6 - - - +
1002G LYS* 1.3 57.4 + - - +
1004G LEU* 3.2 19.8 - - + +
1005G SER* 2.8 28.5 + - - -
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Residues in contact with LYS1002 (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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998G ARG 2.9 15.9 + - - +
999G ALA* 3.8 5.8 - - - +
1001G ALA* 1.3 72.6 - - - +
1003G TYR* 1.3 66.4 + - - +
1005G SER* 3.1 8.5 + - - -
1006G SER* 3.0 25.2 + - - -
1311G VAL* 6.3 0.9 - - + -
1315G HIS* 4.8 28.0 - - + +
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Residues in contact with TYR1003 (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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999G ALA 3.0 15.0 + - - +
1000G CYS* 3.3 14.1 - - - +
1002G LYS* 1.3 76.1 - - - +
1004G LEU* 1.3 68.7 + - + +
1006G SER* 3.1 24.1 - - - -
1088G THR* 5.8 2.5 - - + -
1089G GLY* 4.0 22.6 + - - -
1092G VAL* 3.3 42.0 - - + +
1096G LEU* 4.4 1.8 - - + -
1131G ILE* 4.4 11.2 - - + +
1135G ILE* 3.0 45.8 - - + +
1136G PRO* 5.0 0.2 - - - +
1139G LEU* 5.0 13.6 - - + +
1304G MET* 6.1 1.8 - - + -
1308G LEU* 3.8 16.8 - - + -
1311G VAL* 3.9 28.4 - - + +
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Residues in contact with LEU1004 (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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1000G CYS* 2.9 35.2 + - - +
1001G ALA* 3.2 26.9 - - + +
1003G TYR* 1.3 80.3 - - + +
1005G SER* 1.3 55.6 + - - +
1007G ALA* 2.7 41.4 + - - +
1012G LEU* 3.5 49.3 - - + +
1088G THR* 5.9 0.4 - - - -
1092G VAL* 5.0 0.4 - - - -
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Residues in contact with SER1005 (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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1001G ALA 2.8 20.6 + - - -
1002G LYS* 3.1 12.3 + - - -
1004G LEU* 1.3 77.9 - - - +
1006G SER* 1.3 65.9 + - - +
1007G ALA 2.9 10.4 - - - +
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Residues in contact with SER1006 (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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1002G LYS 3.0 14.6 + - - -
1003G TYR* 3.1 14.0 + - - -
1005G SER* 1.3 77.1 - - - +
1007G ALA* 1.3 56.2 + - - +
1008G GLY 4.2 0.2 + - - -
1091G LYS* 4.8 2.4 - - - +
1092G VAL* 3.6 26.1 - - - -
1095G ARG* 4.3 20.9 - - - +
1096G LEU* 3.9 17.7 - - - +
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Residues in contact with ALA1007 (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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1003G TYR 3.7 0.6 + - - -
1004G LEU* 2.7 29.0 + - - +
1005G SER* 2.9 11.5 - - - +
1006G SER* 1.3 78.2 - - - +
1008G GLY* 1.3 67.8 + - - +
1009G ILE* 3.6 1.4 + - - -
1011G LEU* 3.6 13.2 - - + -
1012G LEU* 4.5 2.6 - - + +
1088G THR* 3.3 26.7 - - - +
1091G LYS* 5.3 2.9 - - - +
1092G VAL* 3.5 16.3 - - + +
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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