Contacts of the helix formed by residues 2262 - 2273 (chain D) in PDB entry 4WVD
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 GLY2262 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B LEU 3.2 16.2 - - - -
452B MET 4.9 1.6 - - - -
2261D LEU* 1.3 74.5 - - - +
2263D LEU* 1.3 67.7 + - - +
2264D GLU* 3.2 4.0 - - - -
2265D ASP* 2.8 25.3 + - - +
2266D ILE* 3.6 7.7 + - - +
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Residues in contact with LEU2263 (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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295B VAL* 4.5 21.1 - - + -
321B LYS* 3.9 28.9 - - + +
324B ALA* 4.1 15.5 - - + -
450B MET* 4.5 13.7 - - + +
451B LEU* 3.5 46.3 + - + +
2262D GLY* 1.3 68.9 - - - -
2264D GLU* 1.3 52.0 + - - +
2266D ILE* 3.0 18.0 + - + +
2267D ILE* 2.6 56.8 + - + +
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Residues in contact with GLU2264 (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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317B ILE* 3.6 23.6 - - + +
321B LYS* 3.4 33.8 + - + +
397B TYR* 5.8 1.9 - - - -
2262D GLY 4.4 2.0 - - - +
2263D LEU* 1.3 78.8 - - - +
2265D ASP* 1.3 52.0 + - - +
2267D ILE* 3.4 10.2 - - - +
2268D ARG* 2.7 68.4 + - - +
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Residues in contact with ASP2265 (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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2260D ASN 4.2 2.6 - - - +
2261D LEU* 3.1 44.3 - - + +
2262D GLY 2.8 16.8 + - - +
2264D GLU* 1.3 68.9 - - - +
2266D ILE* 1.3 59.0 + - - +
2267D ILE 2.9 1.1 - - - -
2268D ARG* 2.8 28.3 + - - +
2269D LYS* 2.5 47.0 + - + +
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Residues in contact with ILE2266 (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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295B VAL* 3.8 29.4 - - + -
296B GLN* 4.4 12.1 + - - +
2261D LEU* 3.8 35.2 - - + -
2262D GLY 4.1 7.9 - - - +
2263D LEU* 3.0 18.9 + - + +
2265D ASP* 1.3 77.8 - - - +
2267D ILE* 1.3 54.7 + - - +
2269D LYS* 3.8 8.2 - - + +
2270D ALA* 2.6 38.6 + - - +
2274D SER* 5.3 0.2 - - - -
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Residues in contact with ILE2267 (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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295B VAL* 5.7 2.0 - - + -
299B VAL* 4.9 9.5 - - + +
317B ILE* 3.8 30.1 - - + +
320B LEU* 3.7 19.1 - - + +
321B LYS* 3.4 43.3 - - + +
324B ALA* 5.6 0.2 - - + -
2263D LEU* 2.6 43.7 + - + +
2264D GLU* 3.4 6.3 - - - +
2266D ILE* 1.3 75.3 - - + +
2268D ARG* 1.3 54.5 + - - +
2270D ALA* 3.5 4.7 - - - +
2271D LEU* 2.7 44.5 + - + +
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Residues in contact with ARG2268 (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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313B HIS* 5.7 3.8 - - + -
317B ILE* 4.2 21.9 - - + +
2264D GLU* 2.7 54.5 + - - +
2265D ASP* 2.8 37.7 + - - +
2267D ILE* 1.3 72.0 - - - +
2269D LYS* 1.3 66.2 + - + +
2271D LEU* 3.1 23.5 + - - +
2272D MET* 3.3 12.3 + - - +
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Residues in contact with LYS2269 (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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2261D LEU* 5.2 13.5 - - + +
2265D ASP* 2.5 29.3 + - + +
2266D ILE* 3.8 8.7 - - + +
2268D ARG* 1.3 73.5 - - + +
2270D ALA* 1.3 51.3 + - - +
2272D MET* 2.7 26.3 + - - -
2273D GLY 2.8 18.4 + - - -
2274D SER* 3.9 19.3 - - - +
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Residues in contact with ALA2270 (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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295B VAL* 5.2 0.2 - - + -
296B GLN* 3.5 29.4 - - + +
299B VAL* 3.3 31.4 - - + +
303B LYS* 5.1 1.7 - - - +
2266D ILE* 2.6 27.1 + - + +
2267D ILE 3.8 2.7 - - - +
2269D LYS* 1.3 73.4 - - - +
2271D LEU* 1.3 58.4 + - - +
2272D MET 3.2 2.0 + - - +
2273D GLY 4.0 7.5 - - - +
2274D SER* 3.7 11.1 + - - +
2275D PHE* 5.5 3.6 - - - -
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Residues in contact with LEU2271 (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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299B VAL* 4.0 12.1 - - + -
303B LYS* 3.8 49.7 + - + +
308B PHE* 4.5 8.7 - - + -
309B GLN* 4.8 7.2 + - - +
313B HIS* 4.6 11.7 - - + +
316B GLN* 4.5 13.5 - - + +
317B ILE* 3.6 32.1 - - + -
320B LEU* 4.2 17.9 - - + -
2267D ILE* 2.7 30.7 + - + +
2268D ARG* 3.1 9.2 + - - +
2270D ALA* 1.3 73.8 - - - +
2272D MET* 1.3 66.9 + - + +
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Residues in contact with MET2272 (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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303B LYS* 5.2 4.2 + - - -
313B HIS* 5.2 12.8 - - - +
2268D ARG 3.3 11.6 + - - +
2269D LYS* 2.7 10.5 + - - +
2270D ALA 4.5 1.4 - - - +
2271D LEU* 1.3 87.4 - - + +
2273D GLY* 1.3 61.8 + - - +
2275D PHE* 4.7 7.6 - - - -
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Residues in contact with GLY2273 (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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296B GLN* 5.7 0.3 - - - +
2269D LYS 2.8 8.9 + - - +
2270D ALA* 4.0 5.2 - - - +
2272D MET* 1.3 79.0 - - - +
2274D SER* 1.3 72.2 + - - +
2275D PHE* 3.1 26.3 - - - -
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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