Contacts of the helix formed by residues 4193 - 4201 (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 SER4193 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4172D TYR* 5.0 0.6 - - - -
4191D GLU 4.0 2.2 + - - -
4192D ILE* 1.3 83.1 - - - +
4194D GLU* 1.3 61.9 + - - +
4195D THR* 3.5 9.5 + - - +
4196D ASN* 3.0 27.0 + - - +
4197D ARG* 3.4 15.8 + - - +
4991D MET* 5.2 5.4 - - - +
4995D ASN* 6.1 0.9 - - - -
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Residues in contact with GLU4194 (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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4172D TYR* 4.0 28.2 - - + +
4192D ILE 3.7 1.6 + - - -
4193D SER* 1.3 74.0 - - - +
4195D THR* 1.3 62.8 + - - +
4196D ASN 3.3 0.2 - - - -
4197D ARG* 3.6 4.4 + - - +
4198D ALA* 3.3 22.3 + - - +
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Residues in contact with THR4195 (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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4193D SER* 3.2 8.8 + - - +
4194D GLU* 1.3 80.0 - - - +
4196D ASN* 1.3 63.4 + - + +
4198D ALA* 3.5 5.9 + - - +
4199D GLN* 3.3 20.8 + - + +
4991D MET* 6.0 5.6 - - + -
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Residues in contact with ASN4196 (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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4192D ILE* 5.0 1.5 - - + +
4193D SER* 3.0 23.1 + - - +
4195D THR* 1.3 79.4 - - + +
4197D ARG* 1.3 64.1 + - - +
4199D GLN* 3.4 7.6 + - - +
4200D TRP* 3.2 26.9 + - - +
4237D ILE* 4.8 4.8 - - - +
4987D MET* 4.4 4.5 + - - +
4988D PHE* 3.2 33.7 + - + +
4991D MET* 3.6 43.0 - - + +
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Residues in contact with ARG4197 (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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4171D PRO 5.9 2.7 - - - +
4172D TYR* 5.6 6.7 - - + -
4192D ILE* 4.8 9.4 - - + +
4193D SER 3.4 12.6 + - - +
4194D GLU* 4.1 7.4 - - - +
4195D THR 3.4 0.4 - - - -
4196D ASN* 1.3 80.2 + - - +
4198D ALA* 1.3 62.3 + - - +
4200D TRP* 3.4 18.3 + - - +
4201D GLU* 3.7 8.5 + - - +
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Residues in contact with ALA4198 (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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4194D GLU 3.3 15.3 + - - +
4195D THR* 3.9 7.0 - - - +
4196D ASN 3.3 0.4 - - - -
4197D ARG* 1.3 79.5 - - - +
4199D GLN* 1.3 61.7 + - - +
4201D GLU* 3.4 21.0 + - - +
4202D MET* 5.2 0.7 - - - +
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Residues in contact with GLN4199 (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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4195D THR 3.3 14.0 + - - +
4196D ASN* 3.9 8.1 - - - +
4197D ARG 3.4 0.2 - - - -
4198D ALA* 1.3 77.5 - - - +
4200D TRP* 1.3 62.3 + - - +
4201D GLU 3.2 0.7 + - - -
4202D MET* 3.5 19.7 - - - +
4205D VAL* 3.5 11.1 - - - +
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Residues in contact with TRP4200 (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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4196D ASN* 3.2 19.3 + - - +
4197D ARG* 3.6 13.7 - - - +
4198D ALA 3.2 0.6 - - - -
4199D GLN* 1.3 78.6 - - - +
4201D GLU* 1.3 57.8 + - + +
4202D MET 3.2 6.3 + - - +
4205D VAL* 3.3 26.6 - - + +
4206D LYS* 5.1 3.1 + - - +
4209D LYS* 5.4 14.8 - - + -
4232D PHE* 5.9 7.2 - + - -
4236D THR* 6.0 5.4 - - + -
4984D ALA* 4.9 9.3 - - + +
4985D ASN* 4.1 34.2 - - + +
4986D TYR 5.4 0.4 - - - -
4987D MET* 4.3 24.2 - - + -
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Residues in contact with GLU4201 (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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4197D ARG 3.7 6.6 + - - +
4198D ALA* 3.4 13.8 + - - +
4199D GLN 3.2 1.2 - - - -
4200D TRP* 1.3 77.3 - - + +
4202D MET* 1.3 57.9 + - - +
4203D PRO* 4.6 1.6 - - - +
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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