Contacts of the strand formed by residues 392 - 400 (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 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A GLN* 3.4 4.1 - - - -
389A PHE 2.9 35.1 + - - -
390A HIS 3.5 0.4 - - - -
391A ASN* 1.3 77.0 - - - +
393A SER* 1.3 73.1 + - - +
394A ILE* 3.9 15.4 + - + +
440A ASP* 3.5 17.8 + - + +
441A VAL* 4.2 11.0 - - + -
559A GLY 4.5 4.8 + - - +
560A VAL* 3.6 13.4 - - + -
561A ARG* 2.8 37.5 + - - +
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG* 3.7 23.1 - - - -
387A PHE 3.5 4.9 - - - -
388A GLN* 4.4 5.6 - - - +
391A ASN 4.1 1.4 + - - -
392A THR* 1.3 69.8 - - - +
394A ILE* 1.3 65.1 + - - +
438A ASN 4.5 1.8 + - - -
439A HIS* 3.5 11.2 - - - -
440A ASP* 2.9 40.8 + - - +
441A VAL 3.0 22.0 + - - -
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Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PHE* 3.6 36.1 - - + -
386A ARG* 3.2 3.8 - - - +
387A PHE* 2.9 69.5 + - + +
389A PHE* 4.0 15.5 - - + -
392A THR* 3.9 17.9 - - + +
393A SER* 1.3 80.7 - - - +
395A CYS* 1.3 63.1 + - - +
396A VAL* 4.3 11.9 - - + -
439A HIS* 3.9 3.3 - - - -
441A VAL* 3.3 26.9 - - + +
443A LEU* 5.4 2.0 - - + -
558A ILE* 5.9 0.2 - - + -
560A VAL* 5.0 2.9 - - + -
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Residues in contact with CYS 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ALA* 4.3 2.0 - - - -
385A ILE 3.7 4.9 - - - -
386A ARG* 4.1 3.4 - - + +
394A ILE* 1.3 74.8 - - - +
396A VAL* 1.3 65.0 + - - +
397A VAL* 4.0 21.1 - - - -
424A PHE* 3.8 33.0 - - - -
436A ILE* 4.0 14.4 - - - +
439A HIS* 3.6 25.5 - - + +
441A VAL 2.9 9.8 + - - +
442A ILE* 3.3 9.1 - - + +
443A LEU 3.0 24.6 + - - +
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Residues in contact with VAL 396 (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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298A CYS* 3.9 39.0 - - + -
349A LEU* 3.4 26.2 - - + +
351A LEU* 5.4 1.6 - - + -
384A ALA* 3.2 5.1 - - - +
385A ILE* 2.9 33.8 + - + +
387A PHE* 4.3 11.2 - - + -
394A ILE* 4.3 16.2 - - + -
395A CYS* 1.3 75.6 - - - +
397A VAL* 1.3 61.9 + - - +
443A LEU* 3.3 19.5 - - + +
445A LEU* 4.3 12.6 - - + -
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 4.7 0.2 - - - -
382A GLY* 5.3 0.2 - - - -
383A VAL 3.5 10.8 - - - +
384A ALA* 4.1 4.7 - - + -
395A CYS* 4.0 9.4 - - - -
396A VAL* 1.3 79.2 - - - +
398A ASN* 1.3 64.0 + - - +
399A SER* 4.8 0.7 - - - -
418A ILE* 4.5 11.7 - - + -
436A ILE* 4.0 29.2 - - + -
442A ILE* 4.7 2.5 - - + -
443A LEU 2.9 8.3 + - - +
444A TRP* 3.5 52.6 - - + +
445A LEU* 2.9 36.3 + - - +
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Residues in contact with ASN 398 (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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300A GLY* 3.5 1.6 - - - -
301A PHE 3.0 20.8 + - - +
302A GLN* 2.9 22.7 + - - -
347A ILE* 3.7 11.9 - - - +
348A MET 2.8 32.1 + - - -
349A LEU* 4.2 10.5 - - + +
382A GLY* 3.2 1.7 - - - -
383A VAL* 2.8 47.9 + - + -
396A VAL 4.4 0.2 + - - -
397A VAL* 1.3 72.8 - - - +
399A SER* 1.3 64.1 + - - +
445A LEU* 3.3 20.8 - - + +
446A GLY* 3.9 0.3 - - - -
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Residues in contact with SER 399 (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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302A GLN* 4.3 0.6 - - - +
347A ILE* 5.0 0.7 - - - -
381A GLY 3.3 10.8 - - - -
382A GLY* 4.4 0.4 - - - -
398A ASN* 1.3 80.1 + - - +
400A HIS* 1.3 59.0 + - - +
401A LEU* 3.8 17.6 - - - +
418A ILE* 4.0 11.0 - - - -
444A TRP* 3.0 29.4 + - - -
445A LEU 3.0 6.3 + - - -
446A GLY* 3.2 2.9 - - - -
447A ASP 3.1 25.1 + - - +
448A LEU* 3.0 16.8 - - - +
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Residues in contact with HIS 400 (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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273A ASN* 4.0 2.2 - - - -
302A GLN* 3.9 20.3 - - + +
303A GLU* 3.3 35.5 + - + +
347A ILE* 3.9 19.5 - - + +
379A ASN 4.0 5.3 + - - -
380A LYS* 3.2 40.1 + - + +
381A GLY* 2.8 35.4 + - - +
399A SER* 1.3 71.2 - - - +
401A LEU* 1.3 66.0 - - - +
447A ASP* 3.3 39.3 + - + -
449A ASN* 3.7 5.1 + - - -
572A PIF 3.6 2.4 + - - -
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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