Contacts of the helix formed by residues 4202 - 4216 (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 MET4202 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4198D ALA 5.2 0.2 - - - +
4199D GLN* 3.5 19.7 - - - +
4200D TRP 3.2 3.2 + - - -
4201D GLU* 1.3 77.6 - - - +
4203D PRO* 1.3 74.8 - - + +
4204D GLN* 4.2 7.2 - - + +
4205D VAL* 3.4 9.9 - - + +
4206D LYS* 3.0 26.4 + - - +
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Residues in contact with PRO4203 (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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4201D GLU 4.6 1.3 - - - +
4202D MET* 1.3 87.6 - - + +
4204D GLN* 1.3 61.0 + - - +
4206D LYS* 4.4 5.2 - - + -
4207D GLU* 3.2 25.8 + - - +
4558D TYR* 5.4 12.9 - - + -
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Residues in contact with GLN4204 (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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4202D MET* 3.2 4.8 - - + +
4203D PRO* 1.3 81.6 - - - +
4205D VAL* 1.3 62.8 + - + +
4207D GLU* 4.4 2.0 - - - +
4208D SER* 3.2 25.3 + - - -
4239D GLU* 4.3 18.2 - - - +
4558D TYR* 4.3 25.7 - - + +
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Residues in contact with VAL4205 (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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4199D GLN 3.5 18.6 - - - +
4200D TRP* 3.3 41.5 - - + +
4202D MET* 3.4 13.4 - - + +
4204D GLN* 1.3 75.3 - - + +
4206D LYS* 1.3 66.2 + - - +
4208D SER* 4.0 5.2 - - - -
4209D LYS* 3.2 24.4 + - - +
4232D PHE* 5.2 2.1 - - - -
4236D THR* 4.8 16.6 - - + +
4239D GLU* 3.3 31.0 - - - +
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Residues in contact with LYS4206 (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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4200D TRP 5.3 2.9 - - - +
4202D MET 3.0 20.5 + - - +
4203D PRO* 4.2 5.6 - - + +
4204D GLN 3.3 0.2 - - - -
4205D VAL* 1.3 78.0 - - + +
4207D GLU* 1.3 64.8 + - - +
4209D LYS* 3.5 5.5 + - - +
4210D ARG* 3.4 19.9 + - - +
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Residues in contact with GLU4207 (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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4203D PRO 3.2 16.4 + - - +
4204D GLN* 4.4 2.2 - - - +
4206D LYS* 1.3 77.2 - - - +
4208D SER* 1.3 62.3 + - - +
4210D ARG* 3.5 6.3 + - - +
4211D GLN* 3.3 21.7 + - - +
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Residues in contact with SER4208 (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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4204D GLN 3.2 20.4 + - - -
4205D VAL* 4.3 5.2 - - - -
4207D GLU* 1.3 75.3 - - - +
4209D LYS* 1.3 63.6 + - - +
4211D GLN* 3.6 6.7 + - - +
4212D PHE* 3.1 22.7 + - - +
4232D PHE* 3.2 20.4 - - - -
4236D THR* 5.5 2.4 - - - +
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Residues in contact with LYS4209 (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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4200D TRP* 5.4 13.5 - - + -
4205D VAL 3.2 20.4 + - - +
4206D LYS* 3.8 6.5 - - - +
4207D GLU 3.3 0.4 - - - -
4208D SER* 1.3 76.5 - - - +
4210D ARG* 1.3 64.3 + - - +
4212D PHE* 3.3 11.7 + - - +
4213D ILE* 3.3 13.3 + - - +
4232D PHE* 3.7 19.7 - - + -
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Residues in contact with ARG4210 (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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4206D LYS 3.4 11.4 + - - +
4207D GLU* 3.5 8.3 + - - +
4208D SER 3.4 0.2 - - - -
4209D LYS* 1.3 77.7 - - - +
4211D GLN* 1.3 62.7 + - - +
4213D ILE* 3.4 15.0 + - - +
4214D PHE* 3.6 11.1 + - - +
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Residues in contact with GLN4211 (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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4207D GLU 3.3 14.6 + - - +
4208D SER* 4.0 6.7 - - - +
4209D LYS 3.3 0.2 - - - -
4210D ARG* 1.3 78.8 - - - +
4212D PHE* 1.3 56.7 + - - +
4214D PHE* 3.5 5.7 + - - +
4215D ASP* 3.0 29.4 + - - +
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Residues in contact with PHE4212 (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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4208D SER 3.1 17.9 + - - +
4209D LYS 3.7 6.1 - - - +
4210D ARG 3.2 0.2 - - - -
4211D GLN* 1.3 76.1 - - - +
4213D ILE* 1.3 67.2 + - + +
4215D ASP* 4.4 7.6 - - + +
4216D VAL* 3.0 34.7 + - + +
4225D LYS 5.3 0.4 - - - -
4228D LEU* 3.7 26.5 - - + -
4229D PHE* 3.5 50.5 - + + -
4232D PHE* 3.6 38.1 - + + -
4957D PHE* 4.1 16.8 - + - -
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Residues in contact with ILE4213 (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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4209D LYS 3.3 10.5 + - - +
4210D ARG* 3.8 10.1 - - - +
4211D GLN 3.3 0.6 - - - -
4212D PHE* 1.3 83.7 - - + +
4214D PHE* 1.3 60.4 + - - +
4216D VAL* 4.3 1.6 - - - +
4217D VAL* 3.5 21.3 + - - +
4948D VAL* 4.2 6.5 - - + +
4957D PHE* 5.0 17.3 - - + -
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Residues in contact with PHE4214 (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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4210D ARG 3.6 8.3 + - - +
4211D GLN* 3.5 8.6 + - - +
4212D PHE 3.2 0.2 - - - -
4213D ILE* 1.3 77.0 - - - +
4215D ASP* 1.3 60.4 + - - +
4216D VAL 3.2 2.4 + - - -
4217D VAL* 3.4 6.2 + - - +
4218D ASN* 2.9 20.4 + - - +
4945D GLN* 4.9 14.4 - - - +
4948D VAL* 4.4 18.1 - - + +
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Residues in contact with ASP4215 (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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4211D GLN 3.0 17.8 + - - +
4212D PHE* 3.4 9.4 + - + +
4214D PHE* 1.3 77.3 - - - +
4216D VAL* 1.3 57.1 + - - +
4218D ASN* 2.8 19.4 + - - +
4219D GLU* 4.5 6.1 + - - +
4228D LEU* 5.5 3.8 - - - +
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Residues in contact with VAL4216 (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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4212D PHE* 3.0 36.9 + - + +
4213D ILE 4.3 2.7 - - - +
4214D PHE 3.2 0.2 - - - -
4215D ASP* 1.3 78.8 - - - +
4217D VAL* 1.3 61.6 + - - +
4219D GLU* 3.8 18.1 - - - +
4225D LYS* 4.4 18.9 - - + +
4228D LEU* 5.7 8.1 - - + -
4957D PHE* 4.5 21.5 - - + -
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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