Contacts of the strand formed by residues 260 - 273 (chain A) in PDB entry 3MTC
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 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A MET* 4.2 11.9 - - + +
259A TYR* 1.3 82.8 - - - +
261A TYR* 1.3 63.4 - - - +
391A ASN* 4.0 25.6 - - + +
561A ARG* 3.1 39.1 + - - -
562A VAL 3.1 13.9 - - - +
563A VAL* 4.2 9.6 - - + -
564A ALA* 5.6 0.4 - - - -
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Residues in contact with TYR 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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1A GOL 3.9 4.5 + - - -
260A THR* 1.3 76.0 - - - +
262A ILE* 1.3 73.4 + - - +
263A GLN* 2.9 39.6 + - + -
560A VAL 3.4 1.0 - - - +
561A ARG* 3.5 7.2 - - - +
562A VAL* 2.8 59.8 + - + +
563A VAL 4.0 0.6 + - - -
564A ALA* 3.9 28.5 - - + -
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Residues in contact with ILE 262 (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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261A TYR* 1.3 81.7 - - - +
263A GLN* 1.3 62.0 + - - +
264A ASN* 4.1 10.1 - - - +
532A ASN* 4.0 28.3 - - - +
559A GLY* 3.7 25.4 - - - +
560A VAL 3.4 15.7 - - - +
561A ARG* 4.0 37.0 - - + +
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Residues in contact with GLN 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GOL 3.2 33.3 + - - -
261A TYR* 2.9 32.9 + - + -
262A ILE* 1.3 74.1 - - - +
264A ASN* 1.3 65.9 + - - +
265A PHE* 3.3 30.0 - - + -
357A HIS* 5.8 0.4 - - - -
560A VAL 2.8 33.6 + - - +
562A VAL* 3.6 17.8 - - + +
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Residues in contact with ASN 264 (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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262A ILE* 4.1 7.4 - - - +
263A GLN* 1.3 80.0 + - - +
265A PHE* 1.3 66.4 + - - +
295A ASP* 4.7 1.2 - - - +
532A ASN* 5.1 0.5 - - - +
557A ASP* 4.6 26.3 + - - +
558A ILE 3.5 4.7 - - - +
559A GLY* 3.4 21.9 + - - -
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Residues in contact with PHE 265 (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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1A GOL 4.0 4.7 - - - -
263A GLN* 3.3 53.4 - - + -
264A ASN* 1.3 75.0 - - - +
266A ARG* 1.3 61.3 + - - +
267A PHE* 3.7 21.8 - - + -
295A ASP* 3.5 24.9 - - + +
357A HIS* 3.7 25.1 - + - -
389A PHE* 3.7 19.7 - + + -
390A HIS* 4.0 18.4 - - - -
556A PHE 3.6 0.5 - - - +
557A ASP* 3.6 6.8 - - - -
558A ILE 2.9 32.0 + - - +
560A VAL* 3.7 22.2 - - + -
562A VAL* 4.1 4.9 - - + -
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Residues in contact with ARG 266 (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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265A PHE* 1.3 71.6 - - - +
267A PHE* 1.3 60.6 + - - +
292A GLN* 3.3 53.3 + - - +
293A ALA 4.7 5.4 - - - +
294A PRO* 3.7 7.6 - - + -
295A ASP* 2.8 49.0 + - - +
296A VAL 3.0 8.8 + - - +
536A LEU* 3.2 27.7 - - + +
555A VAL* 4.0 16.4 - - + +
556A PHE 3.4 8.3 - - - +
557A ASP* 3.2 29.8 + - - +
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Residues in contact with PHE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PHE* 3.7 26.2 - - + -
266A ARG* 1.3 77.2 - - - +
268A PHE* 1.3 60.7 + - - +
294A PRO* 4.9 0.2 - - - -
296A VAL* 3.4 39.5 - - + -
298A CYS* 4.4 4.7 - - - -
387A PHE* 4.5 6.5 - + - -
389A PHE* 4.3 7.4 - + - -
394A ILE* 3.6 37.5 - - + -
443A LEU* 4.4 17.9 - - + -
554A SER 3.8 0.5 - - - +
555A VAL* 3.4 5.9 - - - -
556A PHE* 2.8 41.0 + - + +
558A ILE* 3.5 42.6 - - + -
560A VAL* 4.5 4.7 - - + -
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Residues in contact with PHE 268 (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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266A ARG 4.2 0.4 - - - -
267A PHE* 1.3 74.2 - - - +
269A ALA* 1.3 61.5 + - - +
270A GLY* 3.7 20.4 - - - -
286A TRP* 3.4 27.6 - - - -
287A LEU* 3.7 35.2 - - + -
291A ILE* 3.9 14.8 - - + -
294A PRO* 3.9 11.8 - - + +
296A VAL 2.8 8.3 + - - +
297A TYR* 3.6 29.1 - + + -
298A CYS* 2.8 34.8 + - - +
299A VAL* 4.7 1.8 - - + -
541A HIS* 5.9 0.2 - + - -
553A SER* 3.6 22.9 - - - -
554A SER 3.5 4.5 - - - -
555A VAL* 3.9 21.3 - - + +
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Residues in contact with ALA 269 (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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268A PHE* 1.3 78.3 - - - +
270A GLY* 1.3 58.0 + - - +
298A CYS* 3.3 7.2 - - + -
443A LEU* 4.7 13.7 - - + -
445A LEU* 4.2 15.9 - - + -
526A ILE* 3.4 23.1 - - + +
553A SER* 3.2 4.9 - - - -
554A SER 2.9 37.1 + - - +
556A PHE* 4.3 10.3 - - + -
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Residues in contact with GLY 270 (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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268A PHE* 3.7 10.6 - - - -
269A ALA* 1.3 73.7 - - - +
271A THR* 1.3 59.7 - - - -
286A TRP* 3.7 17.3 - - - -
298A CYS 2.9 10.4 + - - -
299A VAL* 4.8 0.9 - - - -
300A GLY* 2.9 22.7 + - - -
445A LEU* 3.6 12.1 - - - +
526A ILE* 4.6 1.1 - - - -
552A VAL 3.3 10.8 - - - -
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Residues in contact with THR 271 (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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270A GLY* 1.3 74.8 - - - -
272A TYR* 1.3 61.2 + - - +
286A TRP* 3.7 1.3 - - - -
300A GLY 3.3 4.5 - - - -
302A GLN* 3.0 26.5 + - - -
445A LEU* 3.8 13.2 - - - -
446A GLY* 3.3 18.2 - - - +
524A ASP* 4.3 6.8 + - + +
525A ARG 4.0 22.0 - - - +
526A ILE* 4.2 5.6 - - + -
550A LYS 4.7 0.5 - - - +
551A PRO* 3.5 1.4 - - - +
552A VAL* 2.9 50.9 + - + +
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Residues in contact with TYR 272 (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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271A THR* 1.3 78.1 + - - +
273A ASN* 1.3 74.5 + - - +
274A VAL* 3.6 20.9 + - + -
281A GLU* 4.3 1.0 + - - -
283A LEU* 4.7 10.5 - - + -
286A TRP* 3.6 33.4 - + + -
300A GLY 3.0 6.9 + - - -
301A PHE* 3.2 15.4 - + + -
302A GLN* 3.0 21.4 + - - -
322A TRP* 4.2 13.2 - + - -
524A ASP* 5.8 0.4 - - - -
544A LEU* 4.0 16.6 - - + +
546A THR* 3.9 22.9 + - - -
547A SER* 3.8 9.9 + - - -
549A HIS 3.6 21.0 + - - -
550A LYS 4.2 2.5 - - - -
551A PRO* 3.7 33.4 - - + -
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Residues in contact with ASN 273 (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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272A TYR* 1.3 73.6 - - - +
274A VAL* 1.3 52.6 + - - +
275A ASN* 3.0 16.8 + - - +
302A GLN* 3.2 19.7 + - - +
303A GLU* 3.2 38.6 + - - +
400A HIS* 3.8 4.2 + - - -
447A ASP* 2.9 24.0 + - - +
524A ASP* 4.3 4.8 + - - +
547A SER* 2.7 26.5 + - - -
548A ASP* 4.6 0.2 - - - +
549A HIS* 3.4 43.2 + - + +
572A PIF 5.1 0.2 + - - -
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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