Contacts of the strand formed by residues 300 - 304 (chain T) in PDB entry 6MZL
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 ILE 300 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293T TYR 3.2 2.8 - - - +
294T ARG* 3.7 0.4 - - - -
295T MET* 2.8 28.0 + - + -
298T PRO* 2.9 31.6 + - + +
299T ARG* 1.3 84.5 - - - +
301T VAL* 1.3 68.7 + - - +
302T LEU* 3.5 19.5 - - + +
312T LEU* 4.3 7.4 - - + -
313T THR 3.3 15.5 - - - +
315T ALA* 3.7 39.5 - - + +
320T GLU* 3.9 14.1 - - + +
321T ILE* 4.7 2.0 - - + -
324T ALA* 3.7 20.2 - - + -
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Residues in contact with VAL 301 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 5.4 13.9 - - + -
77A LEU* 5.4 13.7 - - + -
292T ILE* 3.8 26.2 - - + -
293T TYR 3.4 3.6 - - - +
294T ARG* 4.1 27.8 - - + +
299T ARG 4.5 1.5 + - - +
300T ILE* 1.3 74.9 - - - +
302T LEU* 1.3 64.4 + - - +
303T LEU* 5.1 6.3 - - + -
311T VAL 3.8 0.3 - - - +
312T LEU* 3.7 1.7 - - - -
313T THR* 2.9 54.8 + - + +
314T GLY* 6.0 1.1 - - - -
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Residues in contact with LEU 302 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291T LEU 2.9 5.2 - - - +
292T ILE* 3.2 5.2 - - - +
293T TYR* 2.9 55.1 + - + +
295T MET* 4.3 9.2 - - + -
300T ILE* 3.5 31.2 - - + +
301T VAL* 1.3 77.6 - - - +
303T LEU* 1.3 64.0 + - - +
304T ILE* 4.1 6.7 - - + -
310T VAL* 3.8 10.5 - - + -
311T VAL 3.2 4.0 - - - +
312T LEU* 3.7 29.4 - - + -
324T ALA* 4.5 2.5 - - + +
328T ILE* 3.7 36.3 - - + -
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Residues in contact with LEU 303 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 5.0 9.0 - - + -
62A CYS* 6.5 0.7 - - - -
69A LEU* 4.3 24.2 - - + -
74A LEU* 5.9 1.8 - - + -
288T PHE* 3.6 35.0 - - + -
291T LEU 3.1 1.8 - - - -
292T ILE* 3.7 22.7 - - + -
301T VAL* 5.1 6.7 - - + +
302T LEU* 1.3 75.0 - - - +
304T ILE* 1.3 61.7 + - - +
305T PHE* 4.6 18.8 - - + -
309T LYS 3.7 2.3 - - - +
310T VAL* 3.3 5.2 - - - -
311T VAL* 2.9 57.0 + - + +
313T THR* 5.9 5.2 - - + -
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Residues in contact with ILE 304 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268T ILE* 3.8 29.8 - - + -
270T LEU* 3.3 27.2 - - + +
273T LEU* 4.7 4.0 - - + -
290T GLY* 3.2 8.5 - - - -
291T LEU* 3.0 58.5 + - + +
293T TYR* 3.9 16.4 - - + -
302T LEU* 4.0 4.9 - - + +
303T LEU* 1.3 76.3 - - - +
305T PHE* 1.3 67.5 + - - +
309T LYS 3.9 2.0 - - - -
310T VAL* 4.2 23.1 - - + -
328T ILE* 4.1 16.2 - - + -
332T LEU* 4.5 4.9 - - + -
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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