Contacts of the strand formed by residues 380 - 387 (chain A) in PDB entry 1C5G
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 PRO 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ASP* 3.6 31.4 - - + +
54A ASN* 3.9 7.9 - - - +
263A PRO* 5.1 0.9 - - - +
270A LEU* 3.5 27.9 - - + +
378A ASP 3.0 14.6 - - - +
379A ARG* 1.3 109.2 + - - +
381A PHE* 1.3 58.9 + - - +
398A GLN* 3.9 15.5 - - + +
399A VAL 2.9 20.6 - - - +
400A MET* 4.1 0.2 - - - -
401A GLU* 4.2 4.7 - - - +
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Residues in contact with PHE 381 (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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258A MET* 6.0 1.3 - - - -
260A ILE* 3.8 23.1 - - + -
261A ALA 3.8 10.5 - - - +
262A ALA* 4.5 5.4 - - + +
270A LEU* 4.2 6.1 - - - -
298A LEU* 4.0 21.1 - - + -
299A PRO* 3.7 21.1 - - + -
301A PHE* 4.2 15.9 - + - -
380A PRO* 1.3 73.2 - - - +
382A LEU* 1.3 71.6 + - - +
383A PHE* 4.2 15.4 + + + -
397A GLY 3.8 0.2 - - - +
398A GLN* 3.2 3.5 - - - -
399A VAL* 2.7 41.2 + - + +
400A MET 3.3 29.6 - - - -
401A GLU* 3.9 25.1 - - + +
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Residues in contact with LEU 382 (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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43A PHE* 4.4 6.3 - - + -
260A ILE* 3.5 1.2 - - - -
261A ALA* 3.1 43.4 + - + +
270A LEU* 4.2 11.7 - - + +
273A LEU* 4.1 22.7 - - + -
274A THR* 4.5 8.3 - - + -
277A LEU* 3.6 28.5 - - + -
285A TRP* 4.5 5.2 - - + -
381A PHE* 1.3 82.7 - - - +
383A PHE* 1.3 66.7 + - - +
384A VAL* 4.7 6.7 - - + -
396A MET* 4.2 19.1 - - + -
397A GLY 3.0 24.2 - - - +
398A GLN* 4.1 13.0 - - + -
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Residues in contact with PHE 383 (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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56A VAL* 3.9 18.8 - - + -
258A MET* 4.0 20.2 - - - -
259A PHE 3.1 11.9 - - - +
260A ILE* 4.9 1.6 - - + -
301A PHE* 4.2 13.9 - + - -
349A ILE* 3.7 32.1 - - + -
381A PHE* 4.3 11.0 - + + -
382A LEU* 1.3 77.8 - - - +
384A VAL* 1.3 73.9 - - - +
385A VAL* 4.3 15.9 - - + -
395A PHE* 4.4 2.2 - - + -
396A MET* 3.3 17.9 - - - +
397A GLY* 3.2 39.8 + - - +
399A VAL* 3.4 33.9 - - + -
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Residues in contact with VAL 384 (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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257A SER 3.6 0.9 - - - +
258A MET* 3.0 5.6 - - - -
259A PHE* 2.7 47.0 + - + +
277A LEU* 5.8 0.9 - - + -
282A ILE* 4.2 26.5 - - + -
285A TRP* 4.9 7.6 - - + -
382A LEU* 4.7 11.2 - - + -
383A PHE* 1.3 82.2 - - - +
385A VAL* 1.3 67.2 + - - +
386A ARG* 3.9 8.5 + - + -
393A VAL* 4.0 23.1 - - + -
395A PHE 3.5 11.4 - - - +
396A MET* 4.4 15.5 - - + -
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Residues in contact with VAL 385 (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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194A PHE* 3.7 33.2 - - + -
251A TYR* 4.1 23.3 - - + +
256A LEU* 4.7 9.9 - - + -
257A SER 3.5 3.4 - - - +
258A MET* 4.2 13.9 - - + -
349A ILE* 5.1 5.2 - - + -
356A THR* 5.2 0.4 - - + -
383A PHE* 4.3 9.6 - - + -
384A VAL* 1.3 75.0 - - - +
386A ARG* 1.3 61.2 + - - +
393A VAL* 3.6 2.8 - - - -
394A LEU* 2.8 30.1 + - + +
395A PHE* 3.1 34.5 + - + -
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Residues in contact with ARG 386 (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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256A LEU* 3.1 12.7 - - - +
257A SER 2.9 34.4 + - - +
259A PHE* 4.1 21.7 - - + -
279A ALA 5.3 2.6 + - - -
282A ILE* 3.9 25.3 - - - +
283A SER* 4.0 30.6 + - - +
286A LYS* 4.2 13.5 - - - +
384A VAL* 4.5 6.7 - - + -
385A VAL* 1.3 75.4 - - - +
387A HIS* 1.3 65.7 + - - +
388A ASN* 2.8 43.6 + - - +
391A GLY* 4.0 25.3 + - - -
392A THR 3.5 14.6 - - - +
393A VAL* 4.5 6.1 - - - +
394A LEU* 4.6 0.4 - - - +
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Residues in contact with HIS 387 (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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104A GLU* 4.2 12.0 + - + -
105A LEU* 3.3 30.0 - - + +
110A ASN* 2.7 29.7 + - - -
114A ILE* 5.6 0.4 - - + -
255A THR* 3.7 8.0 - - + -
256A LEU* 3.6 28.7 - - + +
386A ARG* 1.3 70.8 - - - +
388A ASN* 1.3 54.3 + - - +
389A PRO* 3.8 23.6 - - + -
390A THR* 2.7 34.6 + - + +
391A GLY* 2.7 33.3 + - - -
392A THR 2.9 17.4 + - - +
394A LEU* 4.5 1.3 - - + -
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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