Contacts of the helix formed by residues 2195 - 2203 (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 HIS2195 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2143D TYR* 2.9 37.1 + + + +
2144D THR 4.6 2.0 - - - -
2145D ILE* 4.6 15.8 - - + +
2146D SER* 4.7 11.7 + - - -
2191D VAL* 3.1 37.4 + - + +
2192D PHE* 4.5 3.3 - - - +
2194D GLN* 1.3 96.0 + - + +
2196D PRO* 1.3 64.5 - - - +
2197D ASN 3.2 1.8 - - - +
2198D LEU* 3.3 22.9 + - + +
2199D MET* 3.5 10.2 + - - +
3643D HIS* 4.7 15.6 - - + +
3644D ARG* 5.1 10.6 - - + +
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Residues in contact with PRO2196 (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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2192D PHE 4.8 5.6 - - - +
2193D TYR 4.9 4.0 - - - +
2194D GLN 3.3 13.5 - - - +
2195D HIS* 1.3 82.2 - - - +
2197D ASN* 1.3 67.4 + - - +
2199D MET* 3.2 9.6 + - + +
2200D ARG* 2.9 33.8 + - - +
2243D ILE* 3.8 30.1 - - + -
2244D SER* 4.5 15.3 - - - -
2246D GLN* 6.2 1.6 - - + -
2247D ASN* 4.1 11.8 - - - +
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Residues in contact with ASN2197 (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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2143D TYR* 3.6 33.1 + - + +
2195D HIS 3.2 0.8 - - - -
2196D PRO* 1.3 81.4 - - - +
2198D LEU* 1.3 58.2 + - - +
2200D ARG* 2.5 39.6 + - - +
2201D ALA* 2.9 30.0 + - - +
2246D GLN* 4.9 6.1 - - - +
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Residues in contact with LEU2198 (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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1735D ILE* 3.8 36.1 - - + -
2141D ARG 5.9 0.7 - - - +
2143D TYR* 3.6 36.3 - - + -
2145D ILE* 4.0 20.4 - - + -
2153D THR* 5.3 5.2 - - + -
2156D LEU* 5.8 6.7 - - + -
2157D LEU* 6.2 0.7 - - + -
2191D VAL* 4.8 15.5 - - + -
2195D HIS* 3.3 19.6 + - + +
2196D PRO 3.2 0.4 - - - -
2197D ASN* 1.3 79.0 - - - +
2199D MET* 1.3 56.9 + - - +
2201D ALA* 3.3 4.2 + - + -
2202D LEU* 2.9 46.8 + - + +
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Residues in contact with MET2199 (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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2192D PHE* 4.4 11.7 - - + +
2195D HIS 3.5 8.2 + - - +
2196D PRO* 3.2 12.6 + - + +
2198D LEU* 1.3 79.8 - - - +
2200D ARG* 1.3 60.5 + - - +
2202D LEU 3.7 0.5 + - - -
2203D GLY* 3.1 16.6 + - - -
2204D MET* 3.7 45.1 + - + +
2205D HIS* 4.2 2.8 + - - -
2240D PHE* 4.2 14.6 - - + -
2247D ASN* 5.4 0.4 - - - +
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Residues in contact with ARG2200 (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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2196D PRO* 2.9 14.0 + - - +
2197D ASN* 2.5 40.7 + - - +
2198D LEU 3.3 0.2 - - - -
2199D MET* 1.3 75.9 - - - +
2201D ALA* 1.3 64.4 + - - +
2203D GLY* 3.3 11.3 + - - -
2205D HIS* 3.9 18.4 - - + -
2206D GLU* 5.0 0.2 - - - +
2240D PHE* 4.9 1.3 - - + -
2246D GLN* 3.4 33.9 - - - +
2247D ASN* 3.2 27.3 + - - +
2250D SER* 4.0 21.9 + - - +
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Residues in contact with ALA2201 (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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2140D PRO 3.7 22.9 - - - +
2141D ARG* 4.3 17.9 - - - +
2142D ALA 5.6 0.2 - - - +
2143D TYR* 5.6 4.3 - - + -
2197D ASN 2.9 17.2 + - - +
2198D LEU* 3.9 8.7 - - + +
2200D ARG* 1.3 78.2 - - - +
2202D LEU* 1.3 66.3 + - + +
2203D GLY* 3.4 0.9 + - - -
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Residues in contact with LEU2202 (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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1733D GLU* 4.7 12.8 - - + -
1735D ILE* 3.8 26.9 - - + -
2141D ARG 5.9 1.8 - - - +
2156D LEU* 5.2 6.7 - - + -
2157D LEU* 4.3 14.1 - - + -
2160D LEU* 3.7 29.4 - - + -
2164D ARG* 3.3 24.5 + - - +
2198D LEU* 2.9 35.8 + - + +
2199D MET 4.1 3.1 - - - +
2201D ALA* 1.3 80.1 - - + +
2203D GLY* 1.3 62.4 + - - +
2204D MET* 3.5 17.5 - - + +
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Residues in contact with GLY2203 (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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2199D MET 3.1 8.7 + - - -
2200D ARG 3.3 9.4 + - - -
2201D ALA 3.2 4.3 - - - -
2202D LEU* 1.3 78.3 - - - +
2204D MET* 1.3 64.2 + - - +
2205D HIS* 3.3 4.0 - - - -
2206D GLU* 3.2 31.2 + - - +
2207D THR* 3.2 17.4 + - - +
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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