Contacts of the strand formed by residues 259 - 264 (chain B) in PDB entry 4DHI
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 ILE 259 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ALA 4.7 0.7 - - - +
93B ILE* 3.8 18.6 - - + +
96B GLY* 3.8 24.0 - - - -
97B LEU* 3.7 30.5 - - + +
100B ILE* 4.1 5.4 - - + -
227B THR* 3.7 21.8 - - + +
228B ARG 3.3 2.6 + - - -
229B VAL* 3.3 19.5 - - + +
230B ARG 3.0 23.7 + - - -
257B PRO* 3.9 2.0 - - - +
258B GLU* 1.3 83.3 - - - +
260B THR* 1.3 65.9 + - - +
261B LEU* 3.9 27.1 - - + -
270B VAL* 4.9 4.5 - - + -
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Residues in contact with THR 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B TYR* 3.5 29.5 + - + +
230B ARG* 3.3 21.4 - - + +
232B GLU* 4.1 5.6 - - + -
257B PRO* 4.4 9.7 + - - +
259B ILE* 1.3 76.5 + - - +
261B LEU* 1.3 70.7 + - - +
270B VAL* 3.8 3.6 - - - +
271B ILE* 3.0 55.3 + - + +
273B LYS* 5.4 5.9 - - - +
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Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 3.7 31.6 - - + -
92B ALA* 3.8 27.1 - - + +
93B ILE* 4.0 14.4 - - + -
229B VAL* 4.2 13.7 - - + -
230B ARG 2.9 8.7 + - - +
231B ILE* 4.4 8.3 - - + -
232B GLU* 2.8 29.7 + - - +
259B ILE* 3.9 12.3 - - + -
260B THR* 1.3 81.5 - - - +
262B LEU* 1.3 60.4 + - - +
263B TYR 4.2 0.2 - - - -
268B TYR* 4.1 16.8 - - + -
269B ASP 3.2 14.4 - - - +
270B VAL* 3.8 12.6 - - + -
271B ILE* 3.9 5.6 - - - +
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PHE* 4.4 7.9 - - + -
53B LEU* 3.7 33.4 - - + -
72B LEU* 3.9 24.2 - - + -
79B ILE* 4.2 15.7 - - + -
232B GLU* 3.5 23.3 - - + +
234B MET* 3.9 22.2 - - + +
261B LEU* 1.3 76.3 - - - +
263B TYR* 1.3 62.4 + - - +
264B ARG* 4.0 6.6 + - + +
267B HIS 3.5 1.6 - - - +
268B TYR* 3.4 6.0 - - - -
269B ASP* 2.8 34.8 + - + +
271B ILE* 3.9 19.9 - - + +
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Residues in contact with TYR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B ILE* 4.0 10.3 - - + +
232B GLU 2.9 9.5 + - - -
233B TYR* 3.7 37.5 - + + -
234B MET* 3.2 26.7 + - - +
235B ASP 4.8 0.8 + - - -
238B ALA* 3.8 21.5 - - + -
261B LEU 4.2 0.4 - - - -
262B LEU* 1.3 74.9 - - - +
264B ARG* 1.3 84.5 + - - +
265B PRO* 4.0 13.6 - - + +
266B GLY 4.1 4.8 + - - -
267B HIS 3.3 15.3 - - - -
268B TYR* 3.4 36.6 - + + -
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Residues in contact with ARG 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 3.5 24.3 - - - +
56B GLU* 4.2 6.9 - - - +
58B ASP* 3.7 17.4 + - - -
59B ASN* 3.0 30.2 + - - -
65B PHE* 4.3 4.3 - - + -
81B TYR* 3.8 17.6 - - - -
234B MET* 3.5 29.8 - - + -
262B LEU* 4.0 8.8 + - + +
263B TYR* 1.3 85.0 - - - +
265B PRO* 1.4 82.0 - - + +
266B GLY 3.0 0.9 + - - -
267B HIS* 2.9 53.9 + - + +
269B ASP* 2.8 28.3 + - - -
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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