Contacts of the helix formed by residues 2244 - 2252 (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 SER2244 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2196D PRO* 4.5 17.0 - - - -
2241D CYS 3.8 6.6 - - - +
2242D ARG 3.8 0.2 - - - -
2243D ILE* 1.3 87.0 - - - +
2245D ARG* 1.3 74.6 + - - +
2246D GLN* 2.7 24.4 + - - -
2247D ASN* 3.7 7.4 + - - +
2248D GLN* 3.3 18.9 + - - +
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Residues in contact with ARG2245 (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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2244D SER* 1.3 82.0 + - - +
2246D GLN* 1.3 66.4 + - - +
2248D GLN* 3.2 7.0 + - + +
2249D ARG* 2.9 59.4 + - - +
2283D ASP 6.1 0.2 - - - +
2284D ASN* 3.3 30.0 + - - +
2285D ASN* 4.8 2.6 - - - +
2286D GLU* 3.4 32.1 - - - +
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Residues in contact with GLN2246 (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* 6.2 1.6 - - + -
2197D ASN* 5.0 4.8 - - - +
2200D ARG* 3.4 37.0 - - - +
2244D SER* 2.7 30.3 + - - +
2245D ARG* 1.3 78.7 + - - +
2247D ASN* 1.3 60.3 + - - +
2249D ARG* 3.3 15.3 + - - +
2250D SER* 2.9 32.2 + - - -
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Residues in contact with ASN2247 (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* 5.4 0.2 - - - -
2196D PRO* 4.1 13.4 - - - +
2199D MET* 5.4 0.2 - - - +
2200D ARG* 3.2 26.9 + - - +
2240D PHE* 3.3 59.3 + - + +
2241D CYS* 4.8 2.2 - - - +
2243D ILE* 3.4 23.5 - - - +
2244D SER* 3.7 13.4 + - - +
2245D ARG 3.3 0.4 - - - -
2246D GLN* 1.3 75.6 - - - +
2248D GLN* 1.3 59.3 + - - +
2250D SER* 3.7 5.5 - - - -
2251D MET* 2.9 32.4 + - - +
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Residues in contact with GLN2248 (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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2241D CYS* 4.0 21.6 + - - +
2244D SER 3.3 12.4 + - - +
2245D ARG* 3.2 14.8 + - - +
2247D ASN* 1.3 78.7 - - - +
2249D ARG* 1.3 58.4 + - - +
2251D MET* 3.3 4.4 + - - +
2252D PHE* 2.9 23.7 + - - +
2279D ALA 3.4 9.5 + - - -
2280D SER* 2.9 51.8 + - - +
2282D ILE 4.3 4.0 + - - +
2283D ASP 5.4 2.0 + - - +
2284D ASN* 4.2 14.1 - - + +
2287D LEU* 3.9 19.0 - - + +
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Residues in contact with ARG2249 (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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2245D ARG* 2.9 58.3 + - - +
2246D GLN* 3.8 14.4 - - - +
2248D GLN* 1.3 76.5 - - - +
2250D SER* 1.3 62.8 + - - +
2252D PHE* 3.5 20.6 + - + +
2253D ASP* 4.0 10.6 + - - +
2284D ASN* 5.4 1.8 - - - +
2286D GLU* 4.5 11.3 - - - +
2287D LEU* 5.6 2.7 - - - -
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Residues in contact with SER2250 (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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2200D ARG* 4.0 17.5 + - - +
2205D HIS* 4.4 26.9 + - - -
2240D PHE* 5.6 1.8 - - - -
2246D GLN 2.9 16.7 + - - -
2247D ASN* 3.7 7.6 - - - -
2249D ARG* 1.3 80.0 - - - +
2251D MET* 1.3 60.8 + - - +
2252D PHE 3.6 0.2 + - - -
2253D ASP* 3.6 21.3 + - - +
2254D HIS* 5.0 0.3 + - - +
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Residues in contact with MET2251 (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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2205D HIS* 5.1 15.9 - - - +
2209D MET* 4.0 19.7 - - + -
2237D LEU* 3.7 37.2 - - + -
2240D PHE* 5.3 7.6 - - + -
2241D CYS* 3.7 24.9 - - - -
2247D ASN 2.9 17.9 + - - +
2248D GLN* 4.0 7.0 - - - +
2250D SER* 1.3 72.5 - - - +
2252D PHE* 1.3 64.6 + - - +
2253D ASP 3.1 3.9 + - - -
2254D HIS* 3.3 13.9 + - + +
2255D LEU* 4.3 2.4 + - - -
2258D LEU* 4.0 17.2 - - + +
2276D VAL* 3.9 21.8 - - + -
2280D SER* 5.1 7.0 - - - -
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Residues in contact with PHE2252 (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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2248D GLN* 2.9 23.3 + - - +
2249D ARG* 3.7 15.0 - - + +
2250D SER 3.3 0.6 - - - -
2251D MET* 1.3 77.2 - - - +
2253D ASP* 1.3 66.6 + - - +
2254D HIS 3.2 1.1 + - - -
2255D LEU* 3.2 46.4 + - + +
2280D SER* 5.0 9.0 - - - -
2281D VAL* 5.6 1.3 - - + -
2287D LEU* 3.8 53.6 - - + -
2290D ALA* 5.0 8.7 - - + -
2291D LEU* 4.6 13.2 - - + -
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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