Contacts of the helix formed by residues 995 - 1007 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994H GLU* 1.3 78.1 - - + +
996H PRO* 1.3 69.6 - - + +
998H ARG* 3.2 6.1 + - - +
999H ALA* 2.9 26.1 + - - +
1305H GLU* 5.9 0.4 - - - +
1312H LYS* 5.1 18.0 - - + +
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Residues in contact with PRO 996 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994H GLU* 3.6 11.7 - - + +
995H ILE* 1.3 94.5 - - + +
997H TRP* 1.3 63.6 + - - +
999H ALA* 4.0 5.1 - - + +
1000H CYS* 2.9 28.7 + - - +
1182H ARG* 5.1 6.5 - - - +
1186H ARG* 5.4 8.5 - - - +
1305H GLU* 3.3 37.6 - - - +
1308H LEU* 5.4 4.2 - - + +
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Residues in contact with TRP 997 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994H GLU* 3.3 21.6 + - - +
996H PRO* 1.3 80.7 - - - +
998H ARG* 1.3 59.5 + - - +
1000H CYS* 3.8 3.2 - - - +
1001H ALA* 2.9 31.7 + - - +
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Residues in contact with ARG 998 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994H GLU 3.0 17.2 + - - +
995H ILE* 3.2 6.9 + - - +
997H TRP* 1.3 76.2 - - - +
999H ALA* 1.3 59.6 + - - +
1001H ALA* 3.2 6.5 + - - +
1002H LYS* 2.9 29.6 + - - +
1312H LYS* 6.5 0.9 - - + -
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Residues in contact with ALA 999 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995H ILE 2.9 17.0 + - - +
996H PRO* 4.0 4.5 - - + +
998H ARG* 1.3 78.2 - - - +
1000H CYS* 1.3 57.6 + - - +
1002H LYS* 3.3 6.0 + - - +
1003H TYR* 3.0 26.2 + - - +
1308H LEU* 3.7 32.1 - - + +
1311H VAL* 4.8 3.5 - - - +
1312H LYS* 3.9 27.1 - - + +
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Residues in contact with CYS1000 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996H PRO 2.9 17.5 + - - +
997H TRP* 4.1 3.6 - - - +
999H ALA* 1.3 76.4 - - - +
1001H ALA* 1.3 58.1 + - - +
1003H TYR* 3.3 6.8 + - - +
1004H LEU* 2.9 42.9 + - - +
1139H LEU* 5.9 0.7 - - - -
1304H MET* 3.9 26.5 - - + -
1308H LEU* 3.5 20.5 - - + +
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Residues in contact with ALA1001 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997H TRP 2.9 21.7 + - - +
998H ARG* 3.5 7.6 - - - +
999H ALA 3.2 0.4 - - - -
1000H CYS* 1.3 77.5 - - - +
1002H LYS* 1.3 57.3 + - - +
1004H LEU* 3.2 19.9 - - + +
1005H SER* 2.8 29.4 + - - -
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Residues in contact with LYS1002 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998H ARG 2.9 16.1 + - - +
999H ALA* 3.8 5.6 - - - +
1001H ALA* 1.3 72.6 - - - +
1003H TYR* 1.3 66.1 + - - +
1005H SER* 3.1 9.3 + - - -
1006H SER* 3.0 24.8 + - - -
1311H VAL* 6.3 0.4 - - + -
1315H HIS* 4.8 28.3 - - + +
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Residues in contact with TYR1003 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999H ALA 3.0 14.0 + - - +
1000H CYS* 3.3 14.3 + - - +
1002H LYS* 1.3 75.8 - - - +
1004H LEU* 1.3 68.2 + - + +
1006H SER* 3.1 24.1 - - - -
1088H THR* 5.8 3.1 - - + -
1089H GLY* 4.0 22.4 + - - -
1092H VAL* 3.3 40.1 - - + +
1096H LEU* 4.4 1.6 - - + -
1131H ILE* 4.4 12.1 - - + +
1135H ILE* 3.0 45.7 - - + +
1136H PRO* 5.0 0.2 - - - +
1139H LEU* 5.0 13.0 - - + +
1304H MET* 6.1 2.2 - - + -
1308H LEU* 3.8 15.9 - - + -
1311H VAL* 3.9 28.6 - - + +
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Residues in contact with LEU1004 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000H CYS* 2.9 35.1 + - - +
1001H ALA* 3.2 26.9 - - + +
1003H TYR* 1.3 80.3 - - + +
1005H SER* 1.3 58.4 + - - +
1007H ALA* 2.7 41.6 + - + +
1012H LEU* 3.5 48.1 - - + +
1092H VAL* 5.0 0.4 - - - -
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Residues in contact with SER1005 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001H ALA 2.8 20.1 + - - -
1002H LYS* 3.1 12.3 + - - -
1004H LEU* 1.3 79.1 - - - +
1006H SER* 1.3 64.7 + - - +
1007H ALA 2.9 10.0 - - - +
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Residues in contact with SER1006 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002H LYS 3.0 14.2 + - - -
1003H TYR* 3.1 13.5 + - - -
1005H SER* 1.3 76.4 - - - +
1007H ALA* 1.3 55.7 + - - +
1008H GLY 4.2 0.2 + - - -
1091H LYS* 4.8 2.8 - - - +
1092H VAL* 3.6 25.9 - - - -
1095H ARG* 4.3 21.3 - - - +
1096H LEU* 3.9 17.4 - - - +
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Residues in contact with ALA1007 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003H TYR 3.7 0.6 + - - -
1004H LEU* 2.7 28.8 + - + +
1005H SER* 2.9 12.7 - - - +
1006H SER* 1.3 78.9 - - - +
1008H GLY* 1.3 68.3 + - - +
1009H ILE* 3.6 1.6 + - - -
1011H LEU* 3.6 12.6 - - + -
1012H LEU* 4.8 2.2 - - + -
1088H THR* 3.3 26.5 - - - +
1091H LYS* 5.3 2.9 - - - +
1092H VAL* 3.5 16.8 - - + +
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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