Contacts of the strand formed by residues 251 - 261 (chain A) in PDB entry 3INB
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 MET 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A ASN 5.5 0.4 - - - +
217A SER* 5.3 1.1 - - - -
233A LEU* 4.2 20.4 - - + -
234A VAL* 3.0 21.1 - - - +
235A GLU* 3.9 22.9 - - + +
250A SER* 1.3 81.1 - - - +
252A TYR* 1.3 75.4 + - - +
279A PRO* 4.0 1.6 - - - +
280A VAL* 3.1 32.5 + - + +
282A ASN* 3.3 31.9 - - - +
283A ASP* 3.7 19.3 - - + -
1215A NAG 4.6 8.5 - - - +
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Residues in contact with TYR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.4 3.7 - - - +
234A VAL* 3.1 30.6 + - + +
236A LYS* 3.2 59.1 - - + +
250A SER* 4.2 16.8 - - - -
251A MET* 1.3 83.6 - - - +
253A ARG* 1.3 63.7 + - - +
277A GLU* 4.6 8.3 - - + -
278A GLN* 3.4 18.4 - - - +
279A PRO* 3.4 38.8 - - + -
280A VAL* 3.8 7.4 - - - -
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Residues in contact with ARG 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A SER* 3.4 39.6 + - - -
220A VAL* 5.8 0.4 - - - +
231A THR* 3.0 19.1 + - - +
232A TYR* 3.7 8.3 - - - +
233A LEU* 3.4 21.2 - - + +
252A TYR* 1.3 74.3 - - - +
254A VAL* 1.3 59.9 + - - +
255A PHE* 3.0 28.7 - - + -
276A LEU 3.6 2.4 - - - +
277A GLU* 3.3 2.1 - - - -
278A GLN* 2.9 42.3 + - + +
280A VAL* 3.8 8.4 - - + +
285A SER* 2.7 54.2 + - - +
286A ASN* 3.9 0.6 - - - +
287A CYS* 3.7 24.2 - - - +
300A CYS* 5.6 0.2 - - - -
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 4.9 2.0 - - + -
209A TYR* 5.8 0.7 - - + -
231A THR* 3.3 2.3 - - - -
232A TYR* 2.8 91.4 + - + +
234A VAL* 4.1 14.6 - - + -
253A ARG* 1.3 73.0 - - - +
255A PHE* 1.3 80.7 + - - +
256A GLU* 4.0 1.8 - - + +
275A TYR* 4.1 14.4 - - + -
276A LEU 3.5 2.9 - - - -
277A GLU* 3.8 30.7 - - + +
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Residues in contact with PHE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLY 3.5 5.6 - - - +
231A THR* 3.1 17.9 - - - -
253A ARG* 3.0 31.9 - - + -
254A VAL* 1.3 91.5 - - - +
256A GLU* 1.3 60.0 + - - +
275A TYR* 3.0 24.2 - - - -
276A LEU* 2.9 25.0 + - + +
278A GLN* 4.9 9.0 - - - -
287A CYS* 3.9 0.7 - - - -
296A LEU* 4.8 6.1 - - + -
298A ALA* 4.2 11.2 - - + -
300A CYS* 3.4 29.2 - - - -
322A VAL* 3.0 50.7 - - + -
324A LEU* 3.3 12.9 - - + +
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Residues in contact with GLU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A SER* 2.6 24.6 + - - -
205A LEU* 3.0 16.5 + - + -
206A LEU* 3.0 15.5 + - - +
228A TYR* 3.0 24.9 + - + -
229A GLY* 4.0 1.1 - - - -
230A GLY 2.9 20.2 + - - +
232A TYR* 2.8 34.0 + - + +
254A VAL* 4.0 1.6 - - + +
255A PHE* 1.3 74.4 - - - +
257A VAL* 1.3 62.7 + - - +
272A MET* 3.4 21.6 - - + +
274A ASN 3.8 3.1 - - - -
275A TYR* 3.9 4.5 - - + -
296A LEU* 2.8 20.9 - - - +
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Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A MET* 4.8 1.6 - - + -
228A TYR* 3.4 18.6 - - - +
229A GLY* 3.9 0.4 - - - -
256A GLU* 1.3 77.3 - - - +
258A GLY* 1.3 61.5 + - - +
272A MET* 3.8 2.8 - - - -
273A THR 3.2 14.6 + - - -
274A ASN* 3.0 41.9 + - + +
291A LEU* 4.6 2.9 - - + -
295A LYS 4.8 0.7 - - - -
296A LEU* 3.5 36.6 - - + +
324A LEU* 4.1 10.3 - - + +
325A GLY 3.6 12.1 - - - +
326A VAL* 4.0 18.6 - - + -
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Residues in contact with GLY 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A MET* 3.1 11.8 - - - +
228A TYR* 2.7 39.3 + - - +
257A VAL* 1.3 78.6 - - - +
259A VAL* 1.3 64.4 + - - -
271A HIS 3.4 8.7 - - - -
273A THR* 3.3 13.9 - - - -
326A VAL* 3.5 6.4 - - - +
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A GLY 3.8 9.4 - - - +
227A MET* 5.1 1.8 - - + -
228A TYR* 3.5 3.0 - - - -
258A GLY* 1.3 79.8 - - - +
260A ILE* 1.3 77.1 + - - +
261A ARG* 3.5 20.5 + - + +
269A VAL 3.4 3.8 - - - +
270A PHE* 3.7 0.5 - - - -
271A HIS* 3.0 42.1 + - - +
273A THR* 4.6 6.1 - - + -
294A LEU* 6.5 0.7 - - + -
326A VAL* 4.5 11.2 - - + -
327A TRP* 4.4 25.6 - - + -
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Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A THR* 3.7 35.9 - - + -
226A GLY* 3.0 26.4 + - - +
227A MET* 4.0 18.1 - - - +
228A TYR* 4.5 4.9 - - + -
259A VAL* 1.3 78.5 - - - +
261A ARG* 1.3 63.0 + - - +
268A PRO* 4.4 8.5 - - + -
269A VAL 4.1 3.4 - - - +
270A PHE* 3.9 23.3 - - + -
571A PHE* 3.9 31.6 - - + -
573A TRP* 3.9 20.1 + - + +
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Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A VAL* 3.9 19.0 - - + +
260A ILE* 1.3 80.5 + - - +
262A ASN* 1.3 99.0 + - - +
263A PRO* 3.1 2.8 - - + +
268A PRO* 3.9 1.2 - - - +
269A VAL* 2.9 49.2 + - + +
271A HIS* 4.9 9.2 - - + +
573A TRP* 4.3 4.5 - - - -
1B SO4 3.4 20.7 + - - +
2B SO4 3.3 23.0 + - - -
275B TYR* 3.3 30.9 + - + +
277B GLU* 5.7 1.0 + - - -
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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