Contacts of the helix formed by residues 1081 - 1085 (chain C) in PDB entry 6RIP
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 PRO1081 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ARG* 6.2 0.2 - - - +
33B ARG* 3.1 48.7 - - + +
34B GLY* 6.0 2.0 - - - -
820C GLU* 4.0 7.2 - - - +
1078C LYS* 5.7 2.7 - - - +
1079C ILE 4.2 2.7 - - - +
1080C ASN* 1.3 99.6 - - + +
1082C ILE* 1.3 66.2 + - + +
1083C GLU* 2.9 20.2 - - - +
1084C ASP* 3.0 29.7 + - - +
1085C MET* 4.1 4.1 + - - +
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Residues in contact with ILE1082 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 4.8 4.5 + - - -
48A LEU* 4.6 30.3 - - + +
178A SER* 6.6 0.2 - - - -
819C SER* 5.6 3.4 - - - +
820C GLU* 4.6 9.4 - - + +
821C ARG* 3.9 50.9 - - + +
824C GLN* 4.0 25.6 - - - +
1081C PRO* 1.3 73.5 - - + +
1083C GLU* 1.3 67.3 + - - +
1084C ASP 3.0 0.9 + - - -
1085C MET* 3.5 16.5 + - + +
1093C PRO* 4.1 22.0 - - + +
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Residues in contact with GLU1083 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 3.5 17.7 + - - +
45A ARG* 3.4 57.1 + - + +
48A LEU* 4.3 13.8 - - + +
49A SER* 3.0 35.0 - - - -
33B ARG* 5.2 5.4 + - - +
34B GLY* 5.9 2.2 - - - -
1081C PRO* 2.9 28.6 - - - +
1082C ILE* 1.3 77.6 + - - +
1084C ASP* 1.3 60.3 + - - +
1085C MET 3.4 1.6 + - - +
1215C GLY* 3.4 19.4 - - - +
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Residues in contact with ASP1084 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ARG* 2.2 46.5 + - - -
34B GLY* 5.7 1.2 - - - -
37B HIS* 4.8 5.1 - - - -
807C TRP* 3.6 29.7 + - + -
1080C ASN* 4.7 7.6 - - + +
1081C PRO* 3.0 29.5 + - + +
1083C GLU* 1.3 76.7 - - - +
1085C MET* 1.2 72.1 + - - +
1086C PRO* 3.9 0.2 - - - +
1214C ASP* 4.8 0.7 - - - +
1215C GLY* 4.2 8.3 + - - -
1216C ARG* 4.2 22.4 + - + +
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Residues in contact with MET1085 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 5.6 0.3 + - - -
807C TRP* 4.9 0.9 - - + -
817C LEU* 3.6 20.2 - - + -
819C SER* 3.4 26.9 - - - -
1080C ASN* 3.0 42.8 - - + +
1081C PRO 4.7 2.7 - - - +
1082C ILE* 3.5 8.6 + - + +
1083C GLU 3.4 4.5 + - - +
1084C ASP* 1.2 87.0 - - - +
1086C PRO* 1.3 78.5 - - + +
1087C TYR* 3.3 5.6 + - - +
1093C PRO* 4.2 19.1 - - + -
1094C VAL* 3.2 30.3 - - - +
1095C ASP 4.9 2.5 - - - -
1097C VAL* 4.7 3.6 - - - -
1214C ASP* 5.3 0.2 - - - -
1215C GLY* 3.3 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