Contacts of the helix formed by residues 995 - 1007 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994E GLU* 1.3 80.0 - - + +
996E PRO* 1.3 69.9 - - + +
998E ARG* 3.2 6.6 + - - +
999E ALA* 2.9 25.8 + - - +
1305E GLU* 5.9 0.4 - - - +
1312E LYS* 5.1 18.0 - - + +
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Residues in contact with PRO 996 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994E GLU* 3.6 11.2 - - + +
995E ILE* 1.3 93.4 - - + +
997E TRP* 1.3 63.1 + - - +
999E ALA* 4.0 4.2 - - + +
1000E CYS* 2.9 29.2 + - - +
1182E ARG* 5.1 6.5 - - - +
1186E ARG* 5.4 7.6 - - - +
1305E GLU* 3.3 35.9 - - - +
1308E LEU* 5.4 4.3 - - + +
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Residues in contact with TRP 997 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994E GLU* 3.3 20.1 + - - +
996E PRO* 1.3 80.2 - - - +
998E ARG* 1.3 57.7 + - - +
1000E CYS* 3.8 2.8 - - - +
1001E ALA* 2.9 31.6 + - - +
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Residues in contact with ARG 998 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994E GLU 3.0 16.7 + - - +
995E ILE* 3.7 5.8 - - - +
997E TRP* 1.3 76.5 - - - +
999E ALA* 1.3 58.5 + - - +
1001E ALA* 3.2 6.1 + - - +
1002E LYS* 2.9 29.5 + - - +
1312E LYS* 6.5 0.7 - - + -
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Residues in contact with ALA 999 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995E ILE 2.9 16.7 + - - +
996E PRO* 4.0 4.5 - - + +
998E ARG* 1.3 77.8 - - - +
1000E CYS* 1.3 55.8 + - - +
1002E LYS* 3.3 5.5 + - - +
1003E TYR* 3.0 27.0 + - - +
1308E LEU* 3.7 32.3 - - + +
1309E GLY* 5.6 0.2 - - - -
1311E VAL* 4.8 3.5 - - - +
1312E LYS* 3.9 26.6 - - + +
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Residues in contact with CYS1000 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996E PRO 2.9 18.1 + - - +
997E TRP* 4.1 3.6 - - - +
999E ALA* 1.3 76.6 - - - +
1001E ALA* 1.3 58.9 + - - +
1003E TYR* 3.3 5.6 + - - +
1004E LEU* 2.9 43.0 + - - +
1139E LEU* 5.9 0.9 - - - -
1304E MET* 3.9 26.2 - - + -
1308E LEU* 3.5 19.2 - - + +
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Residues in contact with ALA1001 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997E TRP 2.9 21.0 + - - +
998E ARG* 3.5 6.7 - - - +
1000E CYS* 1.3 77.7 - - - +
1002E LYS* 1.3 56.8 + - - +
1004E LEU* 3.2 19.9 - - + +
1005E SER* 2.8 29.7 + - - -
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Residues in contact with LYS1002 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998E ARG 2.9 15.9 + - - +
999E ALA* 3.8 5.4 - - - +
1001E ALA* 1.3 73.0 - - - +
1003E TYR* 1.3 67.0 + - - +
1005E SER* 3.1 9.1 + - - -
1006E SER* 3.0 24.4 + - - -
1311E VAL* 6.3 0.7 - - + -
1315E HIS* 4.8 28.5 - - + +
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Residues in contact with TYR1003 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999E ALA 3.0 13.8 + - - +
1000E CYS* 3.3 14.6 + - - +
1002E LYS* 1.3 75.2 - - - +
1004E LEU* 1.3 67.3 + - + +
1006E SER* 3.1 24.0 - - - -
1088E THR* 5.8 2.9 - - + -
1089E GLY* 4.0 22.3 + - - -
1092E VAL* 3.3 41.1 - - + +
1096E LEU* 4.4 2.0 - - + -
1131E ILE* 4.4 11.6 - - + +
1135E ILE* 3.0 45.1 - - + +
1136E PRO* 5.0 0.2 - - - +
1139E LEU* 5.0 13.2 - - + -
1304E MET* 6.1 2.0 - - + -
1308E LEU* 3.8 16.8 - - + -
1311E VAL* 3.9 28.8 - - + +
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Residues in contact with LEU1004 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000E CYS* 2.9 35.3 + - - +
1001E ALA* 3.2 26.9 - - + +
1003E TYR* 1.3 80.8 - - + +
1005E SER* 1.3 57.2 + - - +
1007E ALA* 2.7 41.2 + - + +
1012E LEU* 3.5 47.9 - - + +
1088E THR* 5.9 0.4 - - - -
1092E VAL* 5.0 0.2 - - - -
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Residues in contact with SER1005 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001E ALA 2.8 20.1 + - - -
1002E LYS* 3.1 11.9 + - - -
1004E LEU* 1.3 77.0 - - - +
1006E SER* 1.3 66.8 + - - +
1007E ALA 2.9 9.5 - - - +
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Residues in contact with SER1006 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002E LYS 3.0 14.4 + - - -
1003E TYR* 3.1 14.2 + - - -
1005E SER* 1.3 76.3 - - - +
1007E ALA* 1.3 55.6 + - - +
1008E GLY 4.2 0.2 + - - -
1091E LYS* 4.8 2.6 - - - +
1092E VAL* 3.6 26.5 - - - +
1095E ARG* 4.3 19.9 - - - +
1096E LEU* 3.9 17.2 - - - +
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Residues in contact with ALA1007 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003E TYR 3.7 0.4 + - - -
1004E LEU* 2.7 26.9 + - - +
1005E SER* 2.9 11.8 - - - +
1006E SER* 1.3 78.8 - - - +
1008E GLY* 1.3 69.1 + - - +
1009E ILE* 3.6 1.4 + - - -
1011E LEU* 3.6 12.3 - - + -
1012E LEU* 4.5 2.2 - - + +
1088E THR* 3.3 26.9 - - - +
1091E LYS* 5.3 3.4 - - - +
1092E 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