Contacts of the strand formed by residues 552 - 563 (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 VAL 552 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A GLY* 3.3 0.3 - - - -
271A THR* 2.9 42.2 + - + -
286A TRP* 3.2 9.1 + - - -
498A PHE* 4.1 9.2 - - + -
501A THR* 3.7 26.9 - - + -
524A ASP* 3.8 25.1 - - + +
526A ILE* 3.9 11.7 - - + -
538A TYR* 3.7 28.7 - - + -
539A GLN 3.3 11.9 - - - +
540A SER* 4.2 0.4 - - - -
541A HIS* 4.5 1.1 - - - -
550A LYS 4.2 0.2 - - - +
551A PRO* 1.3 78.4 - - - +
553A SER* 1.3 64.8 + - - +
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Residues in contact with SER 553 (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* 3.6 31.9 - - - -
269A ALA 3.2 6.1 - - - -
286A TRP* 4.1 2.0 - - - -
526A ILE* 3.7 3.4 - - - -
537A SER* 5.3 1.0 + - - -
538A TYR* 3.4 5.5 - - - -
539A GLN* 2.8 42.1 + - - +
541A HIS* 2.8 28.9 + - - -
552A VAL* 1.3 76.7 - - - +
554A SER* 1.3 64.3 + - - +
555A VAL* 5.8 1.2 - - - +
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Residues in contact with SER 554 (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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267A PHE 3.8 0.9 - - - +
268A PHE* 3.5 2.6 - - - -
269A ALA* 2.9 34.1 + - - +
526A ILE* 3.8 15.5 - - - -
535A GLN* 2.7 33.3 + - - +
537A SER* 2.8 15.8 + - - -
538A TYR* 4.2 2.9 - - - -
553A SER* 1.3 76.1 - - - +
555A VAL* 1.3 62.8 + - - +
556A PHE* 3.4 20.3 - - - -
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Residues in contact with VAL 555 (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* 4.0 29.8 - - + +
267A PHE 3.4 10.5 - - - +
268A PHE* 3.9 24.7 - - + -
291A ILE* 4.3 22.9 - - + -
294A PRO* 5.6 3.6 - - + -
535A GLN* 3.7 2.9 - - - -
536A LEU* 2.8 44.0 + - + -
537A SER* 3.3 21.8 + - - +
553A SER* 5.8 1.3 - - - +
554A SER* 1.3 79.5 + - - +
556A PHE* 1.3 58.0 + - - +
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Residues in contact with PHE 556 (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 3.6 0.5 - - - +
266A ARG* 3.4 9.0 - - - +
267A PHE* 2.8 39.3 + - + +
269A ALA* 4.3 9.0 - - + -
443A LEU* 4.1 22.4 - - + -
526A ILE* 4.2 17.3 - - + -
528A TRP* 3.4 43.5 - + + -
533A ILE* 3.6 18.8 - - + -
534A THR 3.2 5.4 - - - +
535A GLN* 3.8 22.7 - - + -
536A LEU* 4.4 4.3 - - - -
554A SER* 3.4 30.3 - - - -
555A VAL* 1.3 76.4 - - - +
557A ASP* 1.3 61.6 + - - +
558A ILE* 3.8 19.3 - - + -
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Residues in contact with ASP 557 (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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264A ASN* 4.6 25.1 + - - +
265A PHE 3.6 7.6 - - - +
266A ARG* 3.2 37.2 + - - +
532A ASN 3.5 3.8 - - - +
533A ILE* 3.6 1.0 - - - -
534A THR* 2.8 42.4 + - - +
536A LEU* 4.0 18.0 - - + +
556A PHE* 1.3 70.0 - - - +
558A ILE* 1.3 61.7 + - - +
559A GLY 4.2 0.2 - - - -
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Residues in contact with ILE 558 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A GLN 3.7 0.2 - - - +
264A ASN* 3.9 3.4 - - - -
265A PHE* 2.9 31.6 + - - +
267A PHE* 3.5 46.0 - - + -
394A ILE* 5.9 0.7 - - + -
441A VAL* 4.0 39.3 - - + -
443A LEU* 4.5 11.9 - - + -
531A LYS 5.0 0.2 - - - +
532A ASN 3.4 6.1 - - - +
533A ILE* 4.2 12.1 - - + -
556A PHE* 3.8 16.8 - - + -
557A ASP* 1.3 79.2 - - - +
559A GLY* 1.3 72.2 + - - +
560A VAL* 3.5 12.6 + - + +
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Residues in contact with GLY 559 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A ILE* 3.7 20.6 - - - +
263A GLN 3.7 1.8 - - - -
264A ASN* 3.4 18.3 + - - -
392A THR* 4.5 6.6 + - - +
441A VAL* 5.3 0.9 - - - +
531A LYS 4.8 1.7 - - - +
532A ASN* 2.9 29.8 + - - +
558A ILE* 1.3 76.7 - - - +
560A VAL* 1.3 63.5 + - - +
561A ARG 4.4 0.2 + - - -
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Residues in contact with VAL 560 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A TYR 3.4 1.2 - - - +
262A ILE* 3.4 3.7 - - - -
263A GLN 2.8 39.0 + - - +
265A PHE* 3.7 15.7 - - + -
267A PHE* 4.5 8.7 - - + -
389A PHE* 3.5 38.4 - - + +
390A HIS* 3.9 24.0 - - + -
392A THR* 3.6 13.7 - - + +
394A ILE* 5.0 2.2 - - + -
558A ILE* 3.9 18.4 - - + +
559A GLY* 1.3 76.9 - - - +
561A ARG* 1.3 65.4 + - - +
562A VAL* 3.2 3.7 + - + +
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Residues in contact with ARG 561 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A THR* 3.1 46.4 + - - -
261A TYR* 3.5 13.7 - - - +
262A ILE* 4.0 29.0 - - + +
390A HIS* 3.1 3.9 - - - +
391A ASN* 3.0 45.5 + - + +
392A THR* 2.8 19.4 + - - +
440A ASP* 6.0 0.7 - - - +
560A VAL* 1.3 68.1 - - - +
562A VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 562 (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 12.1 - - - +
260A THR* 3.1 5.2 - - - -
261A TYR* 2.8 63.8 + - + +
263A GLN* 3.6 28.5 - - + +
265A PHE* 4.1 6.1 - - + -
390A HIS* 3.8 36.6 - - + +
560A VAL* 3.6 4.9 - - + +
561A ARG* 1.3 77.0 - - - +
563A VAL* 1.3 74.6 + - - +
565A HIS* 6.2 1.1 - - + +
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Residues in contact with VAL 563 (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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258A MET* 4.0 33.9 - - + -
259A TYR 3.5 9.0 - - - +
260A THR* 4.2 5.2 - - + -
261A TYR* 4.0 2.1 + - - -
390A HIS* 4.9 4.3 + - + +
391A ASN* 3.9 22.0 - - - +
562A VAL* 1.3 85.1 - - - +
564A ALA* 1.3 75.3 + - - +
565A HIS* 3.6 13.5 + - + -
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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