Contacts of the strand formed by residues 380 - 393 (chain A) in PDB entry 3KAS
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 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A GLN* 3.3 6.3 - - - -
192A VAL* 2.8 45.0 + - + +
193A LYS 4.8 1.6 - - - +
194A ASP* 3.9 27.8 - - - +
378A SER 3.6 10.1 - - - +
379A ASN* 1.3 78.9 - - - +
381A LEU* 1.3 67.6 + - - +
382A LYS* 3.6 4.3 + - + +
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Residues in contact with LEU 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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189A LYS* 4.1 24.9 - - + -
190A ILE 3.4 8.7 - - - +
191A GLN* 4.0 18.2 - - + +
309A TYR* 3.1 55.2 - - + +
380A VAL* 1.3 78.7 - - - +
382A LYS* 1.3 60.0 + - - +
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Residues in contact with LYS 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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156A GLU* 5.8 1.4 + - - -
158A GLY 5.8 3.8 + - - -
159A SER* 6.1 2.0 - - - +
189A LYS* 3.5 3.7 - - - -
190A ILE* 2.8 37.5 + - + +
192A VAL* 4.5 26.4 - - + +
380A VAL* 3.6 4.9 + - + +
381A LEU* 1.3 75.8 - - - +
383A GLU* 1.3 71.0 + - - +
384A ILE* 4.2 19.0 - - + +
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Residues in contact with GLU 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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187A PHE* 3.8 22.1 - - + +
188A VAL* 3.3 32.1 + - - +
189A LYS* 3.6 30.9 + - + +
307A ASP* 5.2 0.3 - - - +
382A LYS* 1.3 82.3 - - - +
384A ILE* 1.3 67.0 + - - +
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Residues in contact with ILE 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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157A ALA* 3.4 30.1 - - + +
158A GLY* 4.1 9.4 - - - +
186A HIS 3.6 1.0 - - - +
187A PHE* 3.3 10.5 - - - -
188A VAL* 2.8 46.4 + - + +
190A ILE* 3.5 45.3 - - + -
382A LYS* 4.1 21.1 - - + +
383A GLU* 1.3 80.1 - - - +
385A LYS* 1.3 61.0 + - - +
386A ILE* 3.5 23.2 + - + -
455A ALA* 5.0 0.2 - - + -
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Residues in contact with LYS 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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158A GLY* 3.9 17.7 + - - +
162A ASP* 5.5 0.3 - - - +
163A GLU* 4.5 24.1 + - - +
185A GLN* 3.0 42.0 - - + +
186A HIS 3.5 4.3 - - - -
187A PHE* 3.6 23.1 - - + -
384A ILE* 1.3 73.2 - - - +
386A ILE* 1.3 64.1 + - - +
387A LEU* 4.2 9.8 + - + +
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Residues in contact with ILE 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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157A ALA* 4.7 1.1 - - + -
158A GLY* 4.7 2.0 - - - +
162A ASP* 5.3 0.9 - - - -
184A ASP 4.0 0.2 - - - +
185A GLN* 3.6 1.0 - - - +
186A HIS* 3.0 54.9 + - + +
188A VAL* 3.9 18.6 - - + -
384A ILE* 3.5 33.2 - - + -
385A LYS* 1.3 75.7 - - - +
387A LEU* 1.3 68.5 + - - +
388A ASN* 4.8 3.1 - - - +
454A SER* 3.7 21.1 - - - +
455A ALA* 4.1 10.3 - - + -
461A VAL* 4.5 2.0 - - + -
462A GLY* 3.8 32.3 - - - +
465A GLU* 4.9 0.7 - - + -
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Residues in contact with LEU 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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162A ASP* 5.3 1.6 + - - -
163A GLU* 4.8 17.9 - - + -
166A ALA* 4.5 15.0 - - + -
167A LEU* 5.6 2.9 - - + -
183A ARG* 4.4 39.5 - - + +
184A ASP 3.9 0.7 - - - +
185A GLN* 3.6 35.2 - - + +
385A LYS* 4.2 9.8 + - + +
386A ILE* 1.3 82.9 - - - +
388A ASN* 1.3 64.5 + - - +
389A ILE* 3.7 13.0 + - + -
409A ARG* 2.4 39.4 + - - +
454A SER* 3.7 4.4 - - - -
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Residues in contact with ASN 388 (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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183A ARG* 3.6 4.7 - - - -
184A ASP* 2.9 56.5 + - + +
186A HIS* 4.0 7.4 - - - -
386A ILE* 4.8 2.0 - - - +
387A LEU* 1.3 73.9 - - - +
389A ILE* 1.3 62.1 + - - +
390A PHE* 3.6 19.9 - - + -
452A SER 3.4 3.4 - - - +
453A TRP* 3.5 21.0 - - + -
454A SER* 3.2 24.1 + - - -
462A GLY* 2.9 35.1 + - - -
466A TRP* 4.1 0.2 - - - +
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Residues in contact with ILE 389 (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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166A ALA* 3.6 34.1 - - + +
169A VAL* 4.1 4.5 - - + -
170A GLU* 3.9 32.8 - - + -
173A PHE* 3.9 18.6 - - + -
181A VAL* 5.5 0.7 - - + -
182A TRP 3.9 3.6 - - - +
183A ARG* 4.0 26.9 - - + +
387A LEU* 4.2 16.2 - - + +
388A ASN* 1.3 80.4 - - - +
390A PHE* 1.3 64.9 + - - +
409A ARG* 4.7 2.0 - - - +
450A PHE 3.6 1.0 - - - +
451A ALA* 3.5 2.8 - - - -
452A SER* 2.8 46.9 + - - -
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Residues in contact with PHE 390 (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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173A PHE* 3.9 5.2 - - - -
181A VAL* 3.2 8.1 - - - +
182A TRP* 3.0 72.8 + + + +
184A ASP* 3.4 26.5 - - + -
388A ASN* 3.6 19.7 - - + -
389A ILE* 1.3 75.9 - - - +
391A GLY* 1.3 57.2 + - - +
404A VAL* 5.5 1.1 - - + -
449A ILE* 3.7 22.4 - - + -
450A PHE 3.3 2.9 - - - -
451A ALA* 3.6 23.8 - - + -
453A TRP* 3.5 26.7 - + - -
466A TRP* 3.8 33.0 - + - -
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Residues in contact with GLY 391 (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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173A PHE* 3.7 8.0 - - - -
178A LEU* 3.5 24.9 - - - -
180A LYS 3.6 6.7 - - - -
181A VAL* 4.3 1.3 - - - -
182A TRP* 4.2 1.3 - - - -
390A PHE* 1.3 74.8 - - - +
392A VAL* 1.3 60.0 + - - -
449A ILE* 3.3 7.4 - - - +
450A PHE* 2.8 34.0 + - - -
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Residues in contact with VAL 392 (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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178A LEU* 3.9 3.9 - - - +
179A SER* 2.8 31.6 + - - -
180A LYS* 3.0 35.7 + - + +
182A TRP* 3.8 18.8 - - + -
391A GLY* 1.3 75.3 - - - +
393A ILE* 1.3 75.1 + - - +
394A LYS* 4.1 11.4 - - + +
402A TYR* 5.8 0.7 - - + -
447A SER* 4.1 11.7 - - - -
448A ILE 3.3 11.0 - - - +
449A ILE* 4.0 15.7 - - + -
450A PHE* 5.0 0.2 - - - -
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Residues in contact with ILE 393 (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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178A LEU* 3.9 19.3 - - + -
179A SER* 3.5 6.1 - - - +
392A VAL* 1.3 76.3 - - - +
394A LYS* 1.3 70.6 + - - +
433A PHE* 3.6 33.4 - - + +
434A SER* 3.8 16.8 - - - +
437A VAL* 3.7 29.2 - - + -
444A PRO* 4.5 9.3 - - + +
446A ARG 4.6 0.5 - - - +
447A SER* 3.3 1.2 - - - -
448A ILE* 2.8 40.8 + - + +
450A PHE* 3.6 19.5 - - + -
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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