Contacts of the helix formed by residues 5002 - 5014 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3890D HIS* 3.8 2.1 - - - -
3965D GLN* 3.2 16.0 + - - +
4023D LEU 5.7 0.2 - - - -
4024D SER* 4.4 16.4 - - - -
4027D GLU* 5.0 5.5 - - - +
4188D ILE* 5.4 7.4 - - + -
4992D TYR* 6.2 1.3 - - + -
5001D HIS* 1.3 75.5 - - - +
5003D GLY* 1.3 65.3 + - - +
5004D GLN* 3.6 9.7 + - + +
5005D GLU* 3.4 25.3 - - + +
5006D SER* 3.0 29.6 + - - -
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Residues in contact with GLY5003 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3890D HIS* 4.8 3.4 - - - -
3965D GLN 3.2 24.4 + - - -
3966D GLY* 3.9 13.5 - - - -
3967D PRO* 4.6 11.8 - - - +
4027D GLU* 5.4 5.6 - - - -
5002D THR* 1.3 84.3 + - - +
5004D GLN* 1.3 56.0 + - - -
5006D SER* 4.5 1.8 - - - -
5007D TYR* 3.6 19.6 + - - +
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Residues in contact with GLN5004 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4027D GLU* 5.3 9.8 - - + +
4178D ILE* 5.0 13.3 - - + +
4188D ILE* 4.1 30.7 - - + -
4989D PHE* 5.9 1.3 - - - -
5002D THR* 3.2 9.8 + - + +
5003D GLY* 1.3 77.3 - - - +
5005D GLU* 1.3 63.4 + - - +
5006D SER 3.3 0.4 - - - -
5007D TYR* 3.4 5.7 + - - +
5008D VAL* 3.3 23.9 + - - +
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Residues in contact with GLU5005 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4188D ILE* 5.7 2.0 - - + +
4989D PHE* 5.2 5.2 - - + -
4992D TYR* 4.8 10.8 - - + -
4993D LEU* 3.4 20.9 - - + +
5001D HIS* 3.8 11.7 - - + -
5002D THR* 3.4 28.6 - - + +
5004D GLN* 1.3 78.3 - - - +
5006D SER* 1.3 57.6 + - - +
5008D VAL* 3.3 10.6 - - - +
5009D TRP* 3.2 28.1 + - - +
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Residues in contact with SER5006 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3890D HIS* 3.5 25.6 - - - -
4998D GLU 5.9 0.4 - - - -
5001D HIS* 4.1 8.0 - - - +
5002D THR 3.0 18.8 + - - -
5003D GLY 4.5 2.9 - - - -
5005D GLU* 1.3 76.0 - - - +
5007D TYR* 1.3 59.8 + - - +
5009D TRP* 3.9 7.3 - - - +
5010D LYS* 3.0 29.1 + - - +
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Residues in contact with TYR5007 (chain D).
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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3967D PRO* 6.2 4.0 - - + -
4178D ILE* 4.2 20.0 - - + -
4179D MET 5.0 1.3 - - - -
4180D GLY* 3.3 23.2 - - - -
4181D ALA* 3.3 27.3 + - + +
5003D GLY 3.6 16.7 + - - +
5004D GLN* 3.4 7.3 + - - +
5005D GLU 3.3 0.8 - - - -
5006D SER* 1.3 77.0 - - - +
5008D VAL* 1.3 66.1 + - - +
5010D LYS* 3.4 7.9 + - + +
5011D MET* 3.2 27.1 + - + +
5019D PHE* 6.4 2.9 - - + -
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Residues in contact with VAL5008 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4178D ILE* 4.7 10.3 - - + -
4989D PHE* 3.8 37.2 - - + -
4993D LEU* 4.7 6.1 - - + -
5004D GLN 3.3 13.1 + - - +
5005D GLU* 3.3 15.9 - - - +
5007D TYR* 1.3 81.8 - - + +
5009D TRP* 1.3 61.8 + - - +
5011D MET* 3.4 5.2 + - - +
5012D TYR* 2.9 30.2 + - + +
5019D PHE* 3.8 38.3 - - + +
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Residues in contact with TRP5009 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3748D PHE* 5.6 13.2 - + - -
4993D LEU* 3.7 41.5 - - + -
4994D ILE* 3.7 32.8 - - + -
4998D GLU* 5.2 14.7 - - + +
5005D GLU 3.2 20.6 + - - +
5006D SER* 3.9 7.2 - - - +
5007D TYR 3.3 0.4 - - - -
5008D VAL* 1.3 77.1 - - - +
5010D LYS* 1.3 66.4 + - - +
5012D TYR* 3.4 32.7 + + + +
5013D GLN* 3.4 18.1 + - + +
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Residues in contact with LYS5010 (chain D).
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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5006D SER 3.0 19.3 + - - +
5007D TYR* 3.7 8.3 - - + +
5008D VAL 3.3 0.2 - - - -
5009D TRP* 1.3 81.6 - - - +
5011D MET* 1.3 59.3 + - - +
5013D GLN* 3.7 5.9 + - - +
5014D GLU* 3.7 16.8 + - - +
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Residues in contact with MET5011 (chain D).
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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5007D TYR* 3.2 20.5 + - + +
5008D VAL* 4.0 5.6 - - - +
5009D TRP 3.3 0.2 - - - -
5010D LYS* 1.3 76.4 - - - +
5012D TYR* 1.3 65.4 + - - +
5014D GLU* 3.3 16.4 + - - +
5016D CYS* 2.8 34.1 - - + +
5018D ASP 5.9 1.1 - - - +
5019D PHE* 5.2 14.1 - - + +
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Residues in contact with TYR5012 (chain D).
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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4230D VAL* 3.6 29.3 + - + +
4234D GLU* 5.3 5.0 - - - +
4714D TRP* 4.4 18.7 - + - -
4990D LEU* 4.2 20.6 - - + +
4994D ILE* 5.5 6.1 - - + -
5008D VAL* 2.9 21.7 + - + +
5009D TRP* 3.7 34.1 - + + +
5010D LYS 3.3 0.6 - - - -
5011D MET* 1.3 77.3 - - - +
5013D GLN* 1.3 64.5 + - + +
5014D GLU 3.4 8.0 - - - +
5016D CYS 4.8 1.3 - - - -
5017D TRP* 4.2 25.2 + + - +
5019D PHE* 4.9 11.0 - + + -
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Residues in contact with GLN5013 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5009D TRP* 3.4 18.0 + - + +
5010D LYS* 3.7 5.6 + - - +
5011D MET 3.3 0.4 - - - -
5012D TYR* 1.3 83.1 - - + +
5014D GLU* 1.3 60.7 + - - +
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Residues in contact with GLU5014 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5010D LYS 3.7 11.0 + - - +
5011D MET* 3.3 15.1 + - - +
5012D TYR 3.2 10.6 - - - +
5013D GLN* 1.3 83.4 - - - +
5015D ARG* 1.3 60.5 + - - +
5016D CYS* 3.2 14.9 + - + +
5017D TRP* 3.9 10.0 - - - -
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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