Contacts of the helix formed by residues 4202 - 4216 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4198B ALA 5.2 0.7 - - - +
4199B GLN* 3.5 18.6 - - - +
4200B TRP 3.2 3.2 + - - -
4201B GLU* 1.3 77.3 - - - +
4203B PRO* 1.3 73.0 - - + +
4204B GLN* 3.2 7.0 - - + +
4205B VAL* 3.4 11.7 - - + +
4206B LYS* 3.0 26.2 + - - +
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Residues in contact with PRO4203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4201B GLU 4.6 1.3 - - - +
4202B MET* 1.3 87.6 - - + +
4204B GLN* 1.3 60.0 + - - +
4206B LYS* 3.9 6.0 - - + +
4207B GLU* 3.2 26.9 + - - +
4558B TYR* 5.4 13.2 - - + -
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Residues in contact with GLN4204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4202B MET* 3.2 5.4 - - + +
4203B PRO* 1.3 81.6 - - - +
4205B VAL* 1.3 62.3 + - + +
4207B GLU* 4.3 1.7 - - - +
4208B SER* 3.2 25.5 + - - -
4239B GLU* 4.3 18.8 - - - +
4558B TYR* 4.3 24.8 - - + +
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Residues in contact with VAL4205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4199B GLN 3.5 19.3 - - - +
4200B TRP* 3.3 41.4 - - + +
4202B MET* 3.4 12.8 - - + +
4204B GLN* 1.3 76.3 - - + +
4206B LYS* 1.3 65.0 - - - +
4208B SER* 4.0 4.4 - - - -
4209B LYS* 3.2 24.3 + - - +
4232B PHE* 5.2 2.1 - - - -
4236B THR* 4.8 17.3 - - + +
4239B GLU* 3.3 29.4 - - - +
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Residues in contact with LYS4206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4200B TRP 5.3 3.4 - - - +
4201B GLU* 6.3 0.2 - - - -
4202B MET 3.0 20.0 + - - +
4203B PRO* 4.2 5.2 - - + +
4205B VAL* 1.3 78.0 - - + +
4207B GLU* 1.3 64.5 + - - +
4209B LYS* 3.5 5.5 + - - +
4210B ARG* 3.4 19.8 + - - +
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Residues in contact with GLU4207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4203B PRO 3.2 17.0 + - - +
4204B GLN* 4.4 1.8 - - - +
4206B LYS* 1.3 78.7 - - - +
4208B SER* 1.3 62.5 + - - +
4210B ARG* 3.5 6.4 + - - +
4211B GLN* 3.3 21.8 + - - +
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Residues in contact with SER4208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4204B GLN 3.2 20.5 + - - -
4205B VAL* 4.3 4.7 - - - -
4207B GLU* 1.3 74.9 - - - +
4209B LYS* 1.3 64.1 + - - +
4211B GLN* 3.6 6.3 + - - +
4212B PHE* 3.1 23.6 + - - +
4232B PHE* 3.2 20.4 - - - -
4236B THR* 5.5 2.8 - - - +
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Residues in contact with LYS4209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4200B TRP* 5.4 14.6 - - + -
4205B VAL 3.2 20.2 + - - +
4206B LYS* 3.8 7.0 - - - +
4207B GLU 3.3 0.4 - - - -
4208B SER* 1.3 75.4 - - - +
4210B ARG* 1.3 64.9 + - - +
4212B PHE* 3.3 11.3 + - - +
4213B ILE* 3.3 13.5 + - - +
4232B PHE* 3.7 18.8 - - + -
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Residues in contact with ARG4210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4206B LYS 3.4 10.4 + - - +
4207B GLU* 3.5 8.7 + - - +
4208B SER 3.4 0.4 - - - -
4209B LYS* 1.3 78.3 - - - +
4211B GLN* 1.3 62.5 + - - +
4213B ILE* 3.4 15.0 + - - +
4214B PHE* 3.6 10.6 + - - +
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Residues in contact with GLN4211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4207B GLU 3.3 15.0 + - - +
4208B SER* 4.0 7.2 - - - +
4209B LYS 3.3 0.2 - - - -
4210B ARG* 1.3 79.4 - - - +
4212B PHE* 1.3 57.6 + - - +
4213B ILE 3.3 0.2 - - - -
4214B PHE* 3.5 5.3 + - - +
4215B ASP* 3.0 29.5 + - - +
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Residues in contact with PHE4212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4208B SER 3.1 17.5 + - - +
4209B LYS 3.7 5.6 - - - +
4210B ARG 3.2 0.4 - - - -
4211B GLN* 1.3 75.9 - - - +
4213B ILE* 1.3 67.2 + - + +
4215B ASP* 4.4 7.2 - - + +
4216B VAL* 3.0 36.2 + - + +
4225B LYS 5.3 1.1 - - - -
4228B LEU* 3.7 25.8 - - + -
4229B PHE* 3.5 50.5 - + + -
4232B PHE* 3.6 38.4 - + + -
4957B PHE* 4.1 16.8 - + - -
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Residues in contact with ILE4213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4209B LYS 3.3 10.1 + - - +
4210B ARG* 3.8 10.8 - - - +
4211B GLN 3.3 0.6 - - - -
4212B PHE* 1.3 82.4 - - + +
4214B PHE* 1.3 61.0 + - - +
4216B VAL* 4.3 1.4 - - - +
4217B VAL* 3.5 21.1 + - - +
4948B VAL* 4.2 7.3 - - + +
4957B PHE* 5.0 18.0 - - + -
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Residues in contact with PHE4214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4210B ARG 3.6 8.3 + - - +
4211B GLN* 3.5 8.5 + - - +
4212B PHE 3.2 0.2 - - - -
4213B ILE* 1.3 77.2 - - - +
4215B ASP* 1.3 59.1 + - - +
4216B VAL 3.2 2.9 + - - -
4217B VAL* 3.4 6.6 + - - +
4218B ASN* 2.9 19.8 + - - +
4945B GLN* 4.9 14.4 - - - +
4948B VAL* 4.4 18.6 - - + -
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Residues in contact with ASP4215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4211B GLN 3.0 19.0 + - - +
4212B PHE* 3.4 10.7 + - + +
4214B PHE* 1.3 77.1 - - - +
4216B VAL* 1.3 57.2 + - - +
4218B ASN* 2.8 18.4 + - - +
4219B GLU* 4.5 6.1 + - - +
4228B LEU* 5.5 4.2 - - - +
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Residues in contact with VAL4216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4212B PHE* 3.0 37.1 + - + +
4213B ILE 4.4 2.7 - - - +
4215B ASP* 1.3 78.3 - - - +
4217B VAL* 1.3 62.5 + - - +
4218B ASN 3.5 0.4 - - - -
4219B GLU* 3.8 17.5 - - - +
4225B LYS* 4.4 19.0 - - + +
4228B LEU* 5.7 8.3 - - + -
4957B PHE* 4.5 21.3 - - + -
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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