Contacts of the helix formed by residues 1036 - 1041 (chain C) in PDB entry 5UH6
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 LEU1036 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616C VAL* 5.2 1.6 - - + -
751C HIS* 3.7 33.7 - - + +
877C ARG* 4.0 17.5 - - + +
883C ASP* 3.2 21.8 - - + +
884C LYS 4.9 1.6 - - - +
1032C LYS* 3.6 31.4 - - + +
1033C LEU 3.3 23.1 - - - +
1034C HIS* 4.0 5.1 - - + -
1035C HIS* 1.3 80.1 - - - +
1037C VAL* 1.3 67.1 + - - +
1038C ASP* 4.3 9.6 - - - +
1039C ASP* 2.9 27.3 + - - +
1040C LYS* 3.2 11.6 + - - +
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Residues in contact with VAL1037 (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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880C SER* 3.5 24.9 - - - +
881C ASP 3.5 19.1 - - - +
882C GLY* 3.6 22.0 + - - +
883C ASP* 3.1 4.9 + - - +
1035C HIS 4.2 0.6 + - - -
1036C LEU* 1.3 71.0 - - - +
1038C ASP* 1.3 66.3 + - - +
1040C LYS* 2.9 9.1 + - - +
1041C ILE* 2.9 34.4 + - - +
428D SER* 5.3 0.7 - - - +
429D VAL* 3.9 17.2 - - + +
520D LYS* 4.3 26.2 - - + +
521D ALA* 4.3 9.4 - - + -
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Residues in contact with ASP1038 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842C GLY* 5.1 11.0 - - - +
875C GLN* 5.4 2.7 - - - +
877C ARG* 4.0 38.7 + - - +
878C LYS 5.2 2.4 - - - +
880C SER* 4.0 7.9 + - - -
883C ASP* 4.4 1.4 - - - +
1036C LEU* 3.1 8.3 + - + +
1037C VAL* 1.3 91.7 + - - +
1039C ASP* 1.3 61.6 + - - +
1041C ILE* 4.7 6.0 - - - +
1060C LYS* 3.6 10.0 + - - -
520D LYS* 3.3 34.4 + - - +
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Residues in contact with ASP1039 (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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753C GLU* 5.6 1.0 - - - +
877C ARG* 2.7 40.9 + - - -
1034C HIS* 4.2 20.1 + - - -
1035C HIS* 5.6 0.2 - - - -
1036C LEU* 2.9 19.8 + - - +
1038C ASP* 1.3 78.1 - - - +
1040C LYS* 1.3 65.6 + - + +
1041C ILE 3.4 0.7 - - - -
1060C LYS* 2.6 35.2 + - - +
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Residues in contact with LYS1040 (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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1035C HIS* 3.8 35.6 - - - +
1036C LEU 3.2 19.5 + - - +
1037C VAL 2.9 3.0 + - - +
1039C ASP* 1.3 82.1 - - + +
1041C ILE* 1.3 63.9 + - - +
1042C HIS* 3.6 3.3 + - - +
1060C LYS* 5.3 0.4 - - - +
427D ARG* 3.6 9.2 - - - +
428D SER* 4.2 1.9 - - - -
429D VAL* 3.7 26.9 - - + -
538D GLY 5.5 3.4 - - - +
540D GLN* 3.2 48.5 + - + +
18G A 6.0 5.7 - - - -
1I G 4.9 8.5 + - - -
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Residues in contact with ILE1041 (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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842C GLY* 6.5 1.3 - - - -
1037C VAL 2.9 18.7 + - - +
1038C ASP 4.7 7.6 - - - +
1040C LYS* 1.3 76.0 - - - +
1042C HIS* 1.3 69.4 + - - +
1060C LYS* 3.4 18.8 - - - +
427D ARG 3.6 3.6 - - - -
428D SER* 3.6 21.0 + - - +
444D PRO* 4.4 6.3 - - + -
446D LEU* 4.7 14.4 - - + -
447D MET* 4.1 22.2 - - + +
520D LYS* 3.4 48.2 - - + +
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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