Contacts of the helix formed by residues 5002 - 5014 (chain H) in PDB entry 6X34
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 THR5002 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3890H HIS* 3.8 1.9 - - - -
3965H GLN* 3.2 16.6 + - - -
4023H LEU 5.7 0.2 - - - -
4024H SER* 4.4 16.3 - - - -
4027H GLU* 5.0 4.9 - - - +
4188H ILE* 5.4 7.4 - - + -
4992H TYR* 6.1 1.5 - - + -
5001H HIS* 1.3 74.4 - - - +
5003H GLY* 1.3 65.4 + - - +
5004H GLN* 3.6 9.7 + - + +
5005H GLU* 3.4 24.8 - - + +
5006H SER* 3.0 30.5 + - - -
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Residues in contact with GLY5003 (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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3890H HIS* 4.8 3.8 - - - -
3965H GLN 3.2 24.2 + - - -
3966H GLY* 3.9 13.7 - - - -
3967H PRO* 4.6 11.9 - - - +
4027H GLU* 5.4 5.6 - - - -
5002H THR* 1.3 83.4 + - - +
5004H GLN* 1.3 56.8 + - - -
5006H SER* 4.5 1.7 - - - -
5007H TYR* 3.6 19.8 + - - +
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Residues in contact with GLN5004 (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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4027H GLU* 5.3 10.2 - - + +
4178H ILE* 5.0 13.3 - - + +
4188H ILE* 4.1 29.8 - - + -
4989H PHE* 5.4 1.3 - - - -
5002H THR* 3.2 9.8 + - + +
5003H GLY* 1.3 76.2 - - - +
5005H GLU* 1.3 64.0 + - - +
5006H SER 3.3 0.4 - - - -
5007H TYR* 3.4 5.8 + - - +
5008H VAL* 3.3 23.9 + - - +
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Residues in contact with GLU5005 (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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4188H ILE* 5.7 1.7 - - + +
4989H PHE* 5.2 4.7 - - + -
4992H TYR* 4.8 11.4 - - + -
4993H LEU* 3.4 21.3 - - + +
5001H HIS* 3.8 11.4 - - + -
5002H THR* 3.4 28.2 - - + +
5004H GLN* 1.3 78.8 - - - +
5006H SER* 1.3 58.7 + - - +
5008H VAL* 3.3 11.2 - - - +
5009H TRP* 3.2 27.4 + - - +
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Residues in contact with SER5006 (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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3890H HIS* 3.5 26.0 - - - -
4998H GLU 5.9 0.4 - - - -
5001H HIS* 4.1 8.0 - - - +
5002H THR 3.0 18.5 + - - -
5003H GLY* 4.5 2.9 - - - -
5005H GLU* 1.3 75.6 - - - +
5007H TYR* 1.3 61.1 + - - +
5009H TRP* 3.9 6.5 - - - +
5010H LYS* 3.0 29.5 + - - +
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Residues in contact with TYR5007 (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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3967H PRO* 6.2 4.7 - - + -
4178H ILE* 4.2 19.7 - - + -
4179H MET 5.0 0.9 - - - -
4180H GLY* 3.3 23.4 - - - -
4181H ALA* 3.3 27.8 + - + +
5003H GLY 3.6 17.2 + - - +
5004H GLN* 3.4 6.9 + - - +
5005H GLU 3.3 0.6 - - - -
5006H SER* 1.3 76.8 - - - +
5008H VAL* 1.3 67.4 + - - +
5010H LYS* 3.4 7.1 + - + +
5011H MET* 3.2 26.5 + - + +
5019H PHE* 6.4 3.6 - - + -
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Residues in contact with VAL5008 (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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4178H ILE* 4.7 11.0 - - + -
4989H PHE* 3.8 38.1 - - + -
4993H LEU* 4.7 5.6 - - + -
5004H GLN 3.3 12.7 + - - +
5005H GLU* 3.3 14.4 - - - +
5007H TYR* 1.3 82.6 - - + +
5009H TRP* 1.3 62.2 + - - +
5011H MET* 3.4 5.1 + - - +
5012H TYR* 2.9 30.1 + - + +
5019H PHE* 3.8 38.0 - - + +
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Residues in contact with TRP5009 (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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3748H PHE* 5.6 13.5 - + - -
4993H LEU* 3.7 41.5 - - + -
4994H ILE* 3.7 31.4 - - + -
4998H GLU* 5.2 14.8 - - + +
5005H GLU 3.2 21.0 + - - +
5006H SER* 3.9 7.2 - - - +
5008H VAL* 1.3 77.3 - - - +
5010H LYS* 1.3 66.5 + - - +
5012H TYR* 3.4 32.2 + + + +
5013H GLN* 3.4 17.5 + - + +
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Residues in contact with LYS5010 (chain H).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5006H SER 3.0 18.5 + - - +
5007H TYR* 3.7 8.5 - - + +
5008H VAL 3.3 0.2 - - - -
5009H TRP* 1.3 83.1 - - - +
5011H MET* 1.3 60.3 + - - +
5012H TYR 3.6 0.2 + - - -
5013H GLN* 3.7 5.8 + - - +
5014H GLU* 3.7 16.6 + - - +
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Residues in contact with MET5011 (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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5007H TYR* 3.2 21.7 + - + +
5008H VAL* 4.0 5.6 - - - +
5010H LYS* 1.3 76.8 - - - +
5012H TYR* 1.3 64.5 + - - +
5013H GLN 3.3 0.2 - - - -
5014H GLU* 3.3 15.6 + - - +
5016H CYS* 2.8 33.6 - - + +
5018H ASP 5.9 1.1 - - - +
5019H PHE* 5.2 14.1 - - + +
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Residues in contact with TYR5012 (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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4230H VAL* 3.6 29.9 + - + +
4234H GLU* 5.3 5.4 - - - +
4714H TRP* 4.4 19.4 - + - -
4990H LEU* 4.2 21.3 - - + +
4994H ILE* 5.5 5.4 - - + -
5008H VAL* 2.9 20.7 + - + +
5009H TRP* 3.7 35.0 - + + +
5010H LYS 3.3 0.4 - - - -
5011H MET* 1.3 78.9 - - - +
5013H GLN* 1.3 64.2 + - + +
5014H GLU 3.4 8.0 - - - +
5016H CYS 4.8 1.8 - - - -
5017H TRP* 4.2 24.6 + + - +
5019H PHE* 4.9 10.3 - + + -
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Residues in contact with GLN5013 (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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5009H TRP* 3.4 18.8 + - + +
5010H LYS* 4.1 6.3 - - - +
5011H MET 3.3 0.8 - - - -
5012H TYR* 1.3 83.2 - - + +
5014H GLU* 1.3 60.2 + - - +
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Residues in contact with GLU5014 (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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5010H LYS 3.7 11.0 + - - +
5011H MET* 3.3 15.4 + - - +
5012H TYR 3.2 10.9 - - - +
5013H GLN* 1.3 83.1 - - - +
5015H ARG* 1.3 59.2 + - - +
5016H CYS* 3.2 15.0 + - + +
5017H TRP* 3.9 9.7 - - - -
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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