Contacts of the helix formed by residues 283 - 288 (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 LEU 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A TYR* 4.7 6.3 - - + -
279A PRO* 5.6 0.4 - - + -
281A GLU* 3.5 15.2 + - + +
282A CYS* 1.3 73.2 - - - +
284A ARG* 1.3 60.0 + - - +
285A LEU 3.1 2.5 - - - -
286A TRP* 2.8 27.3 + - + +
287A LEU* 2.8 36.7 + - + +
322A TRP* 4.0 25.4 - - + -
325A ALA* 3.7 46.7 + - + +
326A VAL* 3.8 17.5 - - + +
329A GLY* 4.2 5.8 - - - -
544A LEU* 4.3 15.5 - - + -
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Residues in contact with ARG 284 (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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282A CYS* 3.4 22.3 - - - -
283A LEU* 1.3 76.5 - - - +
285A LEU* 1.3 63.7 + - + +
288A SER* 2.9 68.7 + - - +
289A ASN* 3.3 1.8 + - - +
290A GLY 5.5 1.0 - - - +
328A GLU 4.4 5.2 - - - +
329A GLY* 3.8 17.5 - - - +
330A LEU 5.2 1.1 - - - -
331A HIS* 5.1 4.6 + - - -
332A PRO* 3.5 37.2 - - - +
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Residues in contact with LEU 285 (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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281A GLU* 6.0 1.8 - - + +
282A CYS* 4.1 13.7 + - + +
283A LEU 3.1 1.2 - - - -
284A ARG* 1.3 77.6 - - + +
286A TRP* 1.3 49.2 + - - +
289A ASN* 3.4 31.8 + - - +
541A HIS* 2.7 29.8 + - + +
543A ALA* 4.0 31.0 - - + +
544A LEU* 4.1 23.1 - - + -
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Residues in contact with TRP 286 (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* 3.4 14.0 - + - -
270A GLY* 3.7 12.0 - - - -
271A THR 3.7 21.8 - - - -
272A TYR* 3.6 32.1 - + + -
283A LEU* 2.8 25.1 + - + +
285A LEU* 1.3 80.3 - - - +
287A LEU* 1.3 75.8 + - + +
288A SER 3.6 1.3 - - - -
289A ASN 4.9 1.5 + - - -
291A ILE* 5.7 0.2 - - - +
299A VAL* 3.4 26.5 - - + -
300A GLY 4.1 3.6 - - - -
301A PHE* 3.8 24.5 - + - -
326A VAL* 4.8 0.2 - - + -
541A HIS* 3.5 30.4 - + - -
544A LEU* 3.6 16.8 - - + +
551A PRO* 3.7 19.8 - - + +
552A VAL 3.2 18.9 + - - -
553A SER* 4.1 3.4 - - - -
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Residues in contact with LEU 287 (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 26.7 - - + -
283A LEU* 2.8 27.1 + - + +
286A TRP* 1.3 102.8 - - + +
288A SER* 1.3 56.5 + - - +
289A ASN 4.0 0.2 - - - -
291A ILE* 3.8 8.3 - - - +
297A TYR* 2.6 36.5 + - + -
299A VAL* 4.0 16.2 - - + -
326A VAL* 3.6 48.5 - - + +
329A GLY 3.3 15.3 - - - +
330A LEU* 4.0 2.9 - - + -
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Residues in contact with SER 288 (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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284A ARG* 2.9 50.3 + - - +
287A LEU* 1.3 81.6 - - - +
289A ASN* 1.3 59.4 + - - +
290A GLY 3.6 3.5 + - - -
291A ILE* 4.0 11.0 - - - -
297A TYR* 3.9 1.6 - - - -
329A GLY 2.8 20.0 + - - -
330A LEU 3.8 2.3 + - - -
331A HIS* 3.6 33.2 - - - -
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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