Contacts of the helix formed by residues 4202 - 4216 (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 MET4202 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4198H ALA 5.2 0.4 - - - +
4199H GLN* 3.5 18.4 - - - +
4200H TRP 3.2 3.6 + - - -
4201H GLU* 1.3 76.5 - - - +
4203H PRO* 1.3 74.6 - - + +
4204H GLN* 4.2 7.4 - - + +
4205H VAL* 3.4 10.7 - - + +
4206H LYS* 3.0 26.4 + - - +
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Residues in contact with PRO4203 (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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4201H GLU 4.6 1.8 - - - +
4202H MET* 1.3 88.0 - - + +
4204H GLN* 1.3 61.3 + - - +
4206H LYS* 4.2 4.9 - - + +
4207H GLU* 3.2 25.6 + - - +
4558H TYR* 5.4 12.3 - - + -
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Residues in contact with GLN4204 (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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4202H MET* 3.2 4.4 - - + +
4203H PRO* 1.3 81.9 - - - +
4205H VAL* 1.3 61.9 + - + +
4207H GLU* 4.2 1.9 - - - +
4208H SER* 3.2 25.6 + - - -
4239H GLU* 4.3 18.6 - - - +
4558H TYR* 4.3 25.0 - - + +
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Residues in contact with VAL4205 (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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4199H GLN* 3.5 19.3 - - + +
4200H TRP* 3.3 40.4 - - + +
4202H MET* 3.4 13.9 - - + +
4204H GLN* 1.3 75.8 - - + +
4206H LYS* 1.3 65.8 + - - +
4207H GLU 3.5 0.2 - - - -
4208H SER* 4.0 5.1 - - - -
4209H LYS* 3.2 23.9 + - - +
4232H PHE* 5.2 2.1 - - - -
4236H THR* 4.8 16.8 - - + +
4239H GLU* 3.3 30.7 - - - +
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Residues in contact with LYS4206 (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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4200H TRP 5.3 2.9 - - - +
4202H MET 3.0 20.9 + - - +
4203H PRO* 4.2 5.8 - - + +
4205H VAL* 1.3 79.3 - - + +
4207H GLU* 1.3 63.4 + - - +
4209H LYS* 3.5 5.7 + - - +
4210H ARG* 3.4 19.2 + - - +
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Residues in contact with GLU4207 (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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4203H PRO 3.2 17.2 + - - +
4204H GLN* 4.4 2.5 - - - +
4206H LYS* 1.3 78.9 - - - +
4208H SER* 1.3 62.4 + - - +
4210H ARG* 3.5 6.3 + - - +
4211H GLN* 3.3 21.8 + - - +
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Residues in contact with SER4208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4204H GLN 3.2 19.8 + - - -
4205H VAL* 4.3 5.4 - - - -
4207H GLU* 1.3 76.0 - - - +
4209H LYS* 1.3 63.6 + - - +
4211H GLN* 3.6 5.8 + - - +
4212H PHE* 3.1 23.4 + - - +
4232H PHE* 3.2 19.5 - - - -
4236H THR* 5.5 2.8 - - - +
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Residues in contact with LYS4209 (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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4200H TRP* 5.4 13.9 - - + -
4205H VAL 3.2 20.2 + - - +
4206H LYS* 3.8 6.5 - - - +
4207H GLU 3.3 0.4 - - - -
4208H SER* 1.3 75.8 - - - +
4210H ARG* 1.3 62.7 + - - +
4212H PHE* 3.3 11.4 + - - +
4213H ILE* 3.3 13.9 + - - +
4232H PHE* 3.7 19.7 - - + -
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Residues in contact with ARG4210 (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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4206H LYS 3.4 10.6 + - - +
4207H GLU* 4.0 8.5 - - - +
4208H SER 3.4 0.8 - - - -
4209H LYS* 1.3 77.9 - - - +
4211H GLN* 1.3 61.8 + - - +
4213H ILE* 3.4 14.9 + - - +
4214H PHE* 3.6 11.3 + - - +
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Residues in contact with GLN4211 (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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4207H GLU 3.3 15.2 + - - +
4208H SER* 4.0 7.2 - - - +
4210H ARG* 1.3 78.0 - - - +
4212H PHE* 1.3 58.8 + - - +
4214H PHE* 3.5 6.0 + - - +
4215H ASP* 3.0 28.6 + - - +
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Residues in contact with PHE4212 (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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4208H SER 3.1 18.6 + - - +
4209H LYS 3.7 6.3 - - - +
4210H ARG 3.2 0.4 - - - -
4211H GLN* 1.3 76.5 - - - +
4213H ILE* 1.3 67.3 + - - +
4215H ASP* 4.4 7.4 - - + +
4216H VAL* 3.0 34.8 + - + +
4225H LYS 5.3 0.7 - - - -
4228H LEU* 3.7 27.1 - - + -
4229H PHE* 3.5 50.0 - + + -
4232H PHE* 3.6 37.5 - + + -
4957H PHE* 4.1 15.9 - + - -
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Residues in contact with ILE4213 (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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4209H LYS 3.3 9.9 + - - +
4210H ARG* 3.8 10.8 - - - +
4211H GLN 3.3 0.6 - - - -
4212H PHE* 1.3 82.6 - - + +
4214H PHE* 1.3 60.2 + - - +
4216H VAL* 3.9 1.6 + - - +
4217H VAL* 3.5 20.8 + - - +
4948H VAL* 4.2 7.7 - - + +
4957H PHE* 5.0 17.1 - - + -
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Residues in contact with PHE4214 (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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4210H ARG 3.6 7.4 + - - +
4211H GLN* 3.5 8.3 + - - +
4212H PHE 3.2 0.4 - - - -
4213H ILE* 1.3 77.4 - - - +
4215H ASP* 1.3 61.1 + - - +
4216H VAL 3.2 2.4 + - - -
4217H VAL* 3.4 6.9 + - - +
4218H ASN* 2.9 20.8 + - - +
4945H GLN* 4.9 14.1 - - - +
4948H VAL* 4.4 18.6 - - + -
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Residues in contact with ASP4215 (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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4211H GLN 3.0 17.6 + - - +
4212H PHE* 3.4 10.3 + - + +
4214H PHE* 1.3 78.1 - - - +
4216H VAL* 1.3 57.0 + - - +
4218H ASN* 2.8 19.1 + - - +
4219H GLU* 4.5 5.7 + - - +
4228H LEU* 5.5 4.4 - - - +
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Residues in contact with VAL4216 (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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4212H PHE* 3.0 35.8 + - + +
4213H ILE 4.4 2.9 - - - +
4214H PHE 3.2 0.2 - - - -
4215H ASP* 1.3 79.0 - - - +
4217H VAL* 1.3 61.8 + - - +
4218H ASN 3.5 0.2 - - - -
4219H GLU* 3.8 18.6 - - - +
4225H LYS* 4.4 18.5 - - + +
4228H LEU* 5.7 7.9 - - + -
4957H 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