Contacts of the strand formed by residues 296 - 302 (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 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A ARG 3.0 3.9 + - - +
267A PHE* 3.4 48.7 - - + -
268A PHE 2.8 30.8 + - - +
294A PRO* 3.8 3.8 - - - +
295A ASP* 1.3 88.6 - - + +
297A TYR* 1.3 61.9 + - - +
298A CYS* 4.0 4.0 - - - -
351A LEU* 3.6 23.3 - - + -
352A TYR 3.5 12.1 - - - +
353A VAL* 4.3 14.4 - - + +
387A PHE* 4.8 3.1 - - + -
389A PHE* 4.5 16.2 - - + -
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Residues in contact with TYR 297 (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 32.3 - + + -
287A LEU* 2.6 33.3 + - + -
288A SER* 3.9 0.2 - - - -
294A PRO* 3.4 20.8 - - + +
296A VAL* 1.3 74.7 - - - +
298A CYS* 1.3 60.3 + - - +
299A VAL* 4.1 8.3 - - + -
330A LEU* 3.6 31.0 - - + -
331A HIS* 3.2 16.9 + - - +
336A TYR* 3.5 47.6 - + - -
350A LEU 3.6 0.9 - - - +
351A LEU* 3.5 7.8 - - - +
352A TYR* 3.0 47.9 + - + +
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Residues in contact with CYS 298 (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* 4.4 12.1 - - - -
268A PHE 2.8 17.1 + - - +
269A ALA* 3.3 8.9 - - + -
270A GLY 2.9 25.8 + - - +
296A VAL* 4.0 10.5 - - - -
297A TYR* 1.3 76.5 - - - +
299A VAL* 1.3 63.0 + - - +
349A LEU* 4.5 3.6 - - + -
350A LEU 3.5 5.6 - - - -
351A LEU* 4.0 14.8 - - + -
396A VAL* 3.9 40.2 - - + -
443A LEU* 4.5 6.5 - - + -
445A LEU* 4.3 2.4 - - + +
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Residues in contact with VAL 299 (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* 4.7 2.2 - - + -
270A GLY 3.8 1.8 - - - +
286A TRP* 3.4 37.9 - - + -
287A LEU* 4.0 18.2 - - + -
297A TYR* 4.2 17.5 - - + -
298A CYS* 1.3 82.9 - - - +
300A GLY* 1.3 57.5 + - - +
301A PHE* 4.1 6.0 - - + -
326A VAL* 3.9 32.8 - - + -
348A MET 3.9 0.7 - - - +
349A LEU* 3.5 4.9 - - - +
350A LEU* 2.8 47.4 + - + +
352A TYR* 5.0 2.0 - - + -
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Residues in contact with GLY 300 (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 2.9 14.7 + - - +
271A THR* 3.3 4.4 - - - -
272A TYR* 3.0 23.2 + - - -
286A TRP* 4.1 3.3 - - - -
299A VAL* 1.3 74.7 - - - +
301A PHE* 1.3 65.3 - - - -
302A GLN* 4.1 3.8 - - - -
348A MET 3.3 7.9 - - - -
349A LEU* 4.0 8.0 - - - +
398A ASN* 3.5 10.1 - - - -
445A LEU* 4.1 4.9 - - - -
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Residues in contact with PHE 301 (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* 3.2 10.3 - + + +
274A VAL* 3.7 21.3 - - + -
286A TRP* 3.8 22.9 - + - -
299A VAL* 4.1 9.6 - - + -
300A GLY* 1.3 76.1 - - - -
302A GLN* 1.3 68.2 + - - +
304A LEU* 3.4 21.8 - - + -
322A TRP* 3.5 33.2 - + + -
326A VAL* 3.5 33.7 - - + -
346A GLY 3.9 1.3 - - - +
347A ILE* 3.5 2.3 - - - -
348A MET* 2.9 53.2 + - + +
350A LEU* 4.2 4.9 - - + -
398A ASN* 3.0 15.9 + - - -
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Residues in contact with GLN 302 (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* 3.0 23.6 + - - -
272A TYR 3.0 4.8 + - - -
273A ASN* 3.2 33.9 + - - +
274A VAL* 3.0 26.2 + - - +
300A GLY 4.1 0.2 - - - -
301A PHE* 1.3 84.3 - - - +
303A GLU* 1.3 69.3 + - - +
304A LEU 3.2 3.4 + - - -
346A GLY 3.4 4.9 - - - -
347A ILE* 4.6 2.2 - - + +
398A ASN* 2.9 27.8 + - - +
400A HIS* 3.9 37.5 - - + +
446A GLY* 3.6 3.4 - - - -
447A ASP* 3.5 17.8 - - + +
524A ASP* 4.4 0.9 - - - +
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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