Contacts of the strand formed by residues 267 - 276 (chain B) in PDB entry 1DVM
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 THR 267 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B PHE 3.3 0.2 - - - +
209B ASN* 3.0 8.6 + - - -
210B TYR 2.8 31.2 + - - +
265B ASN 4.4 4.0 + - - -
266B MET* 1.3 77.4 + - - +
268B ARG* 1.3 68.4 + - - +
269B LEU* 3.1 27.6 + - + +
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Residues in contact with ARG 268 (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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207B LYS* 3.5 44.5 + - + +
208B PHE 3.5 5.6 - - - -
209B ASN* 3.7 35.0 + - + +
267B THR* 1.3 74.0 - - - +
269B LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 269 (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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207B LYS* 4.3 0.4 - - - -
208B PHE 3.2 18.0 + - - +
210B TYR* 3.7 38.8 - - + +
267B THR* 3.1 23.4 + - + +
268B ARG* 1.3 74.5 - - - +
270B PRO* 1.3 70.4 - - + +
271B ARG* 3.1 49.6 + - + +
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Residues in contact with PRO 270 (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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206B ASN* 3.4 15.0 - - - +
207B LYS* 3.1 34.9 - - + +
269B LEU* 1.3 84.4 - - + +
271B ARG* 1.3 83.6 + - - +
349B PRO* 4.7 10.6 - - + +
350B GLU 4.3 8.7 + - - -
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Residues in contact with ARG 271 (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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205B THR* 3.0 6.9 + - - -
206B ASN 2.9 31.2 + - - +
208B PHE* 4.1 16.7 - - + -
210B TYR* 5.3 5.3 - - - -
269B LEU* 3.1 56.4 - - + +
270B PRO* 1.3 101.3 + - - +
272B LEU* 1.3 61.3 + - - +
273B LEU* 3.8 1.2 + - - -
349B PRO 5.2 0.9 - - - -
350B GLU* 3.3 46.4 + - - +
351B GLU 4.4 1.3 - - - +
352B ILE* 4.1 33.8 - - + +
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Residues in contact with LEU 272 (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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187B ARG* 6.0 0.9 - - - +
203B ALA* 4.5 8.1 - - + -
204B GLN 4.0 8.7 - - - +
205B THR* 3.3 30.7 - - + -
271B ARG* 1.3 72.8 - - - +
273B LEU* 1.3 64.8 + - - +
274B VAL* 4.0 17.0 - - + -
349B PRO 4.6 4.9 - - - +
350B GLU 2.8 10.8 + - - +
351B GLU* 3.0 35.9 - - + +
352B ILE 3.0 23.1 + - - +
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Residues in contact with LEU 273 (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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179B PHE* 4.1 10.9 - - + -
202B MET 4.0 0.2 - - - +
203B ALA* 3.2 6.8 - - - +
204B GLN 2.9 35.4 + - - +
208B PHE* 3.5 23.8 - - + -
224B LEU* 3.8 27.6 - - + -
226B LEU* 3.7 38.8 - - + -
271B ARG* 3.8 2.4 - - + +
272B LEU* 1.3 72.1 - - - +
274B VAL* 1.3 65.3 + - - +
275B LEU* 3.8 10.7 + - + +
352B ILE* 3.4 15.9 - - + +
354B ILE* 3.8 26.5 - - + -
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Residues in contact with VAL 274 (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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185B HIS* 3.8 5.8 - - + +
187B ARG* 3.3 37.9 - - - +
201B MET* 3.5 27.8 - - + +
202B MET 3.8 3.4 - - - -
203B ALA* 4.1 10.1 - - + -
272B LEU* 4.0 22.0 - - + -
273B LEU* 1.3 77.5 - - - +
275B LEU* 1.3 58.3 + - - +
276B PRO* 3.8 1.7 - - - +
351B GLU* 5.2 0.4 - - - +
352B ILE 2.9 11.8 + - - +
353B ILE* 4.0 17.9 - - + -
354B ILE* 3.0 25.6 + - - +
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Residues in contact with LEU 275 (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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179B PHE* 4.5 5.4 - - + -
201B MET* 4.1 1.1 - - - -
202B MET* 2.9 52.5 + - + +
226B LEU* 3.4 32.8 - - + -
235B MET* 5.7 1.1 - - - -
237B ILE* 4.2 9.0 - - + -
273B LEU* 3.8 15.6 - - + -
274B VAL* 1.3 75.0 - - - +
276B PRO* 1.3 82.9 - - + +
277B LYS 3.1 0.9 + - - -
278B PHE* 5.6 2.0 - - + -
328B VAL* 4.8 9.4 - - + -
354B ILE* 3.3 27.6 - - + -
358B PHE* 4.0 20.4 - - + -
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Residues in contact with PRO 276 (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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189B PHE* 4.1 7.4 - - + -
199B VAL* 4.7 0.2 - - + -
200B PRO 3.8 2.2 - - - +
201B MET* 3.4 25.8 - - + -
274B VAL 3.8 2.2 - - - +
275B LEU* 1.3 94.5 - - + +
277B LYS* 1.3 65.3 + - - +
278B PHE* 3.4 15.4 - - - -
328B VAL* 4.5 0.2 - - - +
354B ILE* 3.1 28.9 - - + +
358B PHE* 3.5 24.9 - - + -
379B PRO* 4.1 23.6 - - + -
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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