Contacts of the strand formed by residues 262 - 271 (chain B) in PDB entry 3F9C
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 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LYS* 2.7 29.7 + - - -
144B TYR 3.6 7.2 - - - +
146B LEU* 4.3 26.5 - - + -
173B ILE* 3.7 28.5 - - + -
236B ILE* 3.7 30.1 - - + -
237B LEU* 4.2 13.5 - - + -
240B ASP* 2.7 31.0 + - + +
258B LEU* 4.8 4.5 - - + +
261B SER* 1.3 78.3 - - - +
263B ASP* 1.3 75.0 + - - +
264B ARG* 3.2 16.0 + - - +
267B ILE* 5.3 1.1 - - + -
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Residues in contact with ASP 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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143B LYS* 4.3 18.9 - - + +
144B TYR 2.8 28.5 + - - +
145B PRO* 4.1 3.5 - - + +
262B ILE* 1.3 72.9 - - - +
264B ARG* 1.3 57.6 + - - +
265B GLU* 3.1 19.3 + - - +
266B LYS* 3.0 64.1 + - + +
267B ILE* 4.4 0.9 - - - +
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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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284A SER 3.8 7.6 + - - -
285A GLU* 3.3 24.0 + - - +
287A GLN* 3.2 35.7 - - + +
309A ARG 5.8 1.8 - - - -
311A PRO* 6.1 2.0 - - + -
143B LYS* 4.8 3.6 - - - +
237B LEU* 2.7 63.6 + - + +
238B ASP* 5.6 1.6 + - - -
240B ASP* 3.4 26.2 + - - +
241B HIS* 3.3 41.6 + - - -
262B ILE* 3.2 14.8 + - + +
263B ASP* 1.3 69.9 + - - +
265B GLU* 1.3 57.3 + - + +
266B LYS 3.5 0.2 - - - -
267B ILE* 3.0 22.7 - - - +
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Residues in contact with GLU 265 (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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287A GLN* 3.3 26.2 - - + +
290A ARG* 3.3 33.6 + - - +
311A PRO* 3.6 32.4 - - + +
312A GLN* 4.3 4.2 - - - +
263B ASP* 3.1 10.8 + - - +
264B ARG* 1.3 78.6 - - - +
266B LYS* 1.3 68.1 + - + +
267B ILE* 3.6 6.0 + - - -
290B ARG* 3.6 25.2 - - - +
396B LEU* 4.8 1.0 - - - +
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Residues in contact with LYS 266 (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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145B PRO* 3.6 17.0 - - + +
146B LEU 2.8 26.0 + - - +
263B ASP* 3.0 40.4 + - + +
265B GLU* 1.3 87.6 + - + +
267B ILE* 1.3 61.4 + - - +
396B LEU* 3.5 33.8 + - + +
397B GLY 3.5 24.2 + - - -
398B LEU* 3.7 19.5 - - + +
399B HIS* 4.8 10.7 + - - -
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Residues in contact with ILE 267 (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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287A GLN* 6.0 0.2 - - + -
146B LEU* 3.3 20.0 - - + +
233B LEU* 3.7 33.7 - - + -
237B LEU* 4.7 9.2 - - + -
262B ILE* 5.3 0.9 - - + -
263B ASP 4.4 3.4 - - - +
264B ARG* 3.0 33.9 - - - +
265B GLU 3.6 4.8 + - - -
266B LYS* 1.3 78.7 - - - +
268B ALA* 1.3 61.1 + - - +
288B ARG* 3.7 19.0 + - + +
289B PHE* 3.2 33.6 - - + -
290B ARG* 2.7 36.4 + - - +
396B LEU* 3.7 3.6 - - - +
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Residues in contact with ALA 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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146B LEU 2.9 9.9 + - - +
147B VAL* 3.2 11.2 - - + -
148B VAL 2.8 24.3 + - - -
266B LYS 4.2 0.2 - - - -
267B ILE* 1.3 75.2 - - - +
269B VAL* 1.3 63.4 + - - +
270B ILE* 5.0 1.3 - - + -
289B PHE* 3.7 8.0 - - - -
291B CYS* 3.3 20.9 - - - +
392B LEU* 3.6 31.0 - - + -
396B LEU* 4.2 6.7 - - + -
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Residues in contact with VAL 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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148B VAL* 3.2 13.0 - - + +
150B SER* 5.2 1.3 - - - -
229B CYS* 4.3 22.9 - - - -
268B ALA* 1.3 73.9 - - - +
270B ILE* 1.3 69.6 + - - +
279B VAL* 3.8 27.2 - - + +
282B THR* 4.4 10.1 - - + -
283B LEU* 4.1 25.8 - - + -
289B PHE* 3.7 28.5 - - + -
291B CYS 3.2 2.6 + - - +
292B GLY* 3.2 7.1 - - - -
293B ILE 3.1 22.3 + - - -
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Residues in contact with ILE 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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147B VAL* 3.8 29.4 - - + -
148B VAL 2.8 6.6 + - - +
149B PHE* 3.2 31.5 - - + -
150B SER* 2.8 24.3 + - - -
163B ILE* 5.4 2.7 - - + -
167B LEU* 4.2 15.3 - - + -
269B VAL* 1.3 82.6 - - - +
271B GLY* 1.3 63.3 + - - +
279B VAL* 3.6 4.0 - - - -
293B ILE* 3.4 44.2 - - + +
295B LEU* 3.9 17.3 - - + -
388B SER* 5.3 4.0 - - - +
392B LEU* 4.2 11.9 - - + -
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Residues in contact with GLY 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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149B PHE* 4.1 7.2 - - - -
150B SER 3.1 15.0 - - - -
270B ILE* 1.3 81.4 - - - +
272B HIS* 1.3 55.3 + - - -
275B GLY 3.3 14.6 - - - -
276B GLY* 3.5 9.0 - - - -
279B VAL* 3.4 1.4 - - - +
293B ILE 3.2 4.2 + - - -
294B ALA 3.8 0.3 - - - -
295B LEU* 2.8 32.0 + - - -
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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