Contacts of the helix formed by residues 1130 - 1136 (chain C) in PDB entry 5GLJ
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 GLY1130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102C TYR* 3.5 20.1 - - - -
1104C LEU 4.7 0.2 - - - -
1105C GLY* 4.6 3.6 - - - -
1127C ALA 3.0 11.8 + - - -
1128C PRO 3.3 2.2 + - - -
1129C GLY* 1.3 78.1 - - - +
1131C PRO* 1.3 77.1 - - - +
1132C ALA 3.4 2.9 - - - -
1133C ASP 3.1 3.9 + - - -
1134C LEU* 2.9 24.8 + - - +
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Residues in contact with PRO1131 (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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1096C LEU* 3.7 16.1 - - + +
1097C LYS 3.3 23.1 - - - +
1099C ASP* 3.9 11.7 - - + -
1102C TYR* 3.6 12.8 - - + -
1103C GLY 3.2 27.6 - - - +
1104C LEU* 3.4 15.0 - - - +
1130C GLY* 1.3 81.8 - - - +
1132C ALA* 1.3 63.1 + - - +
1134C LEU* 3.3 8.6 + - + +
1135C ASP* 2.9 25.3 + - - +
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Residues in contact with ALA1132 (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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1094C VAL* 6.0 0.2 - - - -
1096C LEU* 4.1 13.2 - - + -
1104C LEU 3.1 15.4 + - - +
1105C GLY 3.8 14.1 + - - +
1106C PHE* 4.0 3.4 - - + -
1126C VAL* 4.0 8.6 - - + +
1130C GLY 3.4 0.6 - - - -
1131C PRO* 1.3 77.9 - - - +
1133C ASP* 1.3 61.4 + - - +
1135C ASP* 3.5 2.8 + - - +
1136C GLY* 3.2 17.0 + - - -
1137C CYS 4.3 3.1 + - - -
1138C LEU* 3.8 38.8 + - + +
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Residues in contact with ASP1133 (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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1105C GLY 4.8 0.2 + - - -
1126C VAL* 3.5 17.8 - - + +
1127C ALA 3.1 22.9 + - - +
1128C PRO* 3.5 7.3 - - - +
1129C GLY* 2.8 23.1 + - - +
1130C GLY 3.1 5.8 + - - +
1132C ALA* 1.3 80.0 - - - +
1134C LEU* 1.3 66.8 + - - +
1136C GLY* 3.1 15.8 + - - -
1138C LEU 5.8 0.2 - - - -
1139C LYS* 5.8 1.7 + - - -
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Residues in contact with LEU1134 (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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1129C GLY* 3.6 32.1 - - - +
1130C GLY 2.9 20.2 + - - +
1131C PRO* 3.8 6.5 - - + +
1133C ASP* 1.3 82.0 - - - +
1135C ASP* 1.3 62.8 + - - +
1136C GLY* 3.4 1.4 + - - -
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Residues in contact with ASP1135 (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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1094C VAL* 3.5 19.4 - - - +
1095C ASN 4.0 12.9 + - - +
1096C LEU* 3.6 12.8 - - + -
1131C PRO 2.9 17.7 + - - +
1132C ALA* 3.7 4.4 - - - +
1134C LEU* 1.3 77.1 - - - +
1136C GLY* 1.3 58.1 + - - +
1137C CYS* 3.3 26.9 + - - +
1138C LEU 4.6 0.5 + - - -
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Residues in contact with GLY1136 (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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1132C ALA 3.2 4.7 + - - -
1133C ASP 3.1 16.0 + - - -
1134C LEU 4.3 0.9 - - - -
1135C ASP* 1.3 78.3 - - - +
1137C CYS* 1.3 58.5 + - - +
1138C LEU 3.8 1.1 - - - -
1139C LYS* 3.2 28.3 + - - -
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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