Contacts of the strand formed by residues 334 - 340 (chain A) in PDB entry 1C3B
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 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A VAL* 5.0 0.2 - - + -
33A ILE 3.3 14.4 - - - +
34A TYR* 3.8 29.2 - - + -
35A GLN 5.0 0.4 - - - +
238A LEU* 4.1 3.8 - - - +
328A PHE* 3.2 4.7 - - - +
329A ILE* 2.8 41.6 + - + +
332A LYS* 3.1 21.7 - - + +
333A GLU* 1.3 79.6 - - - +
335A GLY* 1.3 59.2 + - - +
357A LEU* 3.8 31.5 - - + +
360A LEU* 3.9 23.6 - - + +
361A GLN* 3.5 24.9 - - + +
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Residues in contact with GLY 335 (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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32A VAL* 3.5 8.1 - - - +
33A ILE* 2.8 36.9 + - - +
234A VAL* 4.3 8.5 - - - -
327A ALA 3.2 11.9 - - - -
328A PHE* 3.8 7.2 - - - -
334A LEU* 1.3 77.6 - - - +
336A ILE* 1.3 64.8 + - - +
357A LEU* 3.8 6.9 - - - +
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Residues in contact with ILE 336 (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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30A VAL* 4.4 9.9 - - + -
31A ALA 3.3 13.9 - - - +
32A VAL* 4.6 3.1 - - + -
33A ILE* 4.7 1.2 - - - +
234A VAL* 4.6 1.7 - - - +
325A TYR* 5.1 0.7 - - + -
326A VAL* 3.5 2.4 - - - +
327A ALA* 2.9 39.6 + - + +
335A GLY* 1.3 75.8 - - - +
337A VAL* 1.3 79.1 + - - +
338A MET* 4.1 24.2 - - + -
353A ALA* 4.0 23.1 - - + +
356A ILE* 3.9 40.4 - - + -
357A LEU* 4.1 13.7 - - + -
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Residues in contact with VAL 337 (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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30A VAL* 3.2 6.6 - - - +
31A ALA* 3.0 33.2 + - + +
33A ILE* 4.8 2.2 - - + -
227A ILE* 3.7 23.5 - - + +
230A MET* 3.7 28.5 - - + +
231A ALA* 4.6 4.0 - - - +
234A VAL* 3.4 27.8 - - + -
325A TYR 3.5 9.4 - - - +
326A VAL* 4.4 8.7 - - + -
336A ILE* 1.3 81.7 - - - +
338A MET* 1.3 67.8 + - - +
339A LEU* 3.7 16.6 - - + -
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Residues in contact with MET 338 (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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16A ILE* 4.6 5.2 - - - -
19A LEU* 5.4 0.4 - - - -
28A MET* 3.5 26.0 - - + -
29A ALA 3.6 4.9 - - - -
30A VAL* 4.4 4.0 - - + -
323A GLY 4.0 0.8 - - - +
324A SER* 3.2 5.9 - - - -
325A TYR* 3.0 55.9 + - + +
336A ILE* 4.1 19.3 - - + -
337A VAL* 1.3 79.8 - - - +
339A LEU* 1.3 64.2 + - - +
344A TYR* 4.8 10.5 - - - +
349A ARG* 3.5 12.8 - - - +
352A ALA* 4.4 9.6 - - - -
353A ALA* 3.1 41.1 - - + -
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Residues in contact with LEU 339 (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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28A MET* 3.2 6.7 - - - +
29A ALA 2.9 34.6 + - - +
60A PHE* 3.7 42.9 - - + -
62A LEU* 3.9 18.4 - - + -
225A SER 4.6 2.2 - - - +
226A THR 4.1 4.5 - - - -
227A ILE* 3.8 40.8 - - + +
230A MET* 4.3 8.7 - - + -
323A GLY 4.0 2.2 - - - -
324A SER* 3.8 17.7 - - - -
325A TYR 5.1 0.4 - - - +
326A VAL* 5.9 0.7 - - + -
337A VAL* 3.7 13.0 - - + -
338A MET* 1.3 83.7 - - - +
340A ALA* 1.3 60.4 - - - +
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Residues in contact with ALA 340 (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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25A ILE* 3.7 25.1 - - + -
27A GLY 3.5 5.6 - - - +
28A MET* 4.3 7.9 - - - -
60A PHE* 3.9 5.6 - - - -
322A PHE* 3.2 10.4 - - - -
323A GLY 3.0 34.1 + - - +
338A MET 5.8 0.2 - - - -
339A LEU* 1.3 76.1 - - - +
341A ASN* 1.3 59.4 + - - +
342A LYS 3.2 6.3 - - - +
344A TYR* 4.0 19.7 - - + +
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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