Contacts of the strand formed by residues 419 - 433 (chain A) in PDB entry 5C7Z
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 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ARG* 3.5 43.1 - - + +
171A ASN 2.9 12.5 + - - +
172A GLU* 3.2 13.4 - - + +
173A LEU 2.9 28.2 + - - +
417A ASP 4.4 6.7 - - - +
418A VAL* 1.3 75.0 - - - +
420A LYS* 1.3 62.0 + - - +
421A TRP* 3.4 35.2 - - + +
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Residues in contact with LYS 420 (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 LEU* 3.6 19.3 - - + -
404A LEU* 3.0 26.1 + - + +
405A LYS* 5.3 0.8 - - - +
406A VAL* 4.5 4.7 - - - -
415A ASP* 3.0 49.2 + - - -
416A HIS* 5.5 1.4 - - - +
418A VAL* 3.7 19.4 + - + +
419A ILE* 1.3 80.8 - - - +
421A TRP* 1.3 68.1 + - - +
4B SER* 3.4 11.8 + - - -
5B ILE* 3.4 43.5 + - + +
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Residues in contact with TRP 421 (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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170A ARG* 5.2 2.9 - - - -
172A GLU* 2.8 28.0 + - + -
173A LEU* 3.0 20.6 + - - +
174A PHE* 3.3 37.6 - + + -
175A LEU* 2.8 26.7 + - - +
419A ILE* 3.4 20.2 - - + +
420A LYS* 1.3 78.5 - - - +
422A VAL* 1.3 63.3 + - - +
2B TYR* 3.7 27.4 - - + -
3B LYS* 3.3 26.0 - - - -
4B SER* 3.7 23.1 - - - -
5B ILE* 3.9 7.0 - - - +
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Residues in contact with VAL 422 (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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175A LEU* 3.2 18.2 - - + +
177A VAL* 4.3 3.1 - - + -
401A VAL* 4.0 28.0 - - + +
421A TRP* 1.3 76.8 - - - +
423A ARG* 1.3 69.4 + - - +
424A TYR* 4.0 27.3 - - + +
1B GLN 3.9 0.7 - - - +
2B TYR* 3.5 4.6 - - - -
3B LYS* 2.8 39.7 + - + +
4B SER 4.6 2.5 - - - +
5B ILE* 3.6 26.5 - - + -
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Residues in contact with ARG 423 (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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175A LEU 2.8 7.5 + - - +
176A ASP* 2.9 41.0 + - + +
177A VAL* 2.9 27.4 + - - +
178A LEU* 5.6 1.0 - - - +
203A LYS* 3.6 9.1 - - - +
422A VAL* 1.3 76.6 - - - +
424A TYR* 1.3 67.3 + - - +
425A ILE* 4.0 20.8 - - + +
1B GLN* 3.3 60.8 + - + +
2B TYR* 3.1 29.0 + - + -
3B LYS* 6.0 0.4 - - - +
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Residues in contact with TYR 424 (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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177A VAL* 3.5 35.2 - - + +
393A PRO* 3.3 27.8 + - - +
394A PHE* 3.5 23.8 - - - +
395A ALA* 4.1 12.8 - - + -
399A LEU* 3.5 20.2 - - + -
400A LYS* 3.5 15.3 - - + +
401A VAL* 3.0 31.9 + - - +
422A VAL* 4.0 24.7 - - + +
423A ARG* 1.3 79.7 - - - +
425A ILE* 1.3 68.1 + - - +
426A GLY 4.1 0.4 - - - -
1B GLN* 4.9 3.6 + - - +
3B LYS* 5.2 10.5 - - - +
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Residues in contact with ILE 425 (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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177A VAL 3.0 8.6 + - - +
178A LEU* 3.4 31.5 - - + +
179A GLU* 3.1 23.9 + - - +
391A GLU* 3.7 38.4 - - + +
392A VAL 3.7 2.2 - - - +
394A PHE 4.5 0.9 - - - -
395A ALA* 6.1 0.2 - - - -
423A ARG* 4.0 36.8 - - + +
424A TYR* 1.3 78.7 - - - +
426A GLY* 1.3 59.6 + - - +
427A ARG* 4.0 7.2 + - + +
1B GLN* 4.3 12.8 - - - +
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Residues in contact with GLY 426 (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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179A GLU* 3.3 7.6 - - - -
390A PHE* 4.8 0.8 - - - -
391A GLU* 3.3 4.7 - - - +
392A VAL* 2.8 46.2 + - - +
394A PHE 3.6 13.9 + - - -
395A ALA* 5.3 0.2 - - - -
396A PRO* 4.0 11.4 - - - -
425A ILE* 1.3 73.9 - - - +
427A ARG* 1.3 60.2 + - - +
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Residues in contact with ARG 427 (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* 4.1 14.8 + - - +
179A GLU* 2.7 36.9 + - - +
180A SER* 3.1 25.1 - - - +
181A VAL* 2.7 32.0 + - - +
197A SER 5.5 0.8 + - - -
199A ARG* 5.8 6.1 - - - +
390A PHE* 3.4 12.6 - - - +
391A GLU* 4.6 9.4 - - + -
425A ILE* 4.4 7.0 + - + +
426A GLY* 1.3 75.7 - - - +
428A SER* 1.3 72.7 + - - +
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Residues in contact with SER 428 (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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180A SER* 4.6 0.9 + - - -
181A VAL 3.7 6.5 - - - -
388A MET 3.9 6.7 - - - -
389A ASN* 2.8 36.4 + - - +
390A PHE* 3.1 42.3 + - - -
427A ARG* 1.3 85.4 + - - +
429A GLY* 1.3 67.1 + - - +
431A TYR* 4.2 4.5 - - - -
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Residues in contact with GLY 429 (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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180A SER* 3.9 9.9 - - - -
181A VAL 3.0 14.1 + - - +
182A ASN* 3.2 12.6 - - - -
388A MET 4.4 1.2 - - - +
389A ASN* 3.5 14.9 - - - +
427A ARG 3.5 1.6 + - - -
428A SER* 1.3 79.4 - - - +
430A ILE* 1.3 62.6 + - - -
431A TYR* 3.6 2.6 + - - +
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Residues in contact with ILE 430 (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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182A ASN* 2.9 23.9 + - + +
183A LEU 2.7 37.7 + - - +
184A LEU* 6.0 2.0 - - + -
195A HIS* 6.0 3.1 - - + -
429A GLY* 1.3 69.8 - - - -
431A TYR* 1.3 55.2 + - - +
432A GLU* 3.9 30.1 - - + +
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Residues in contact with TYR 431 (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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181A VAL* 3.7 26.5 - - + +
183A LEU* 3.5 32.9 - - + +
285A LEU* 3.6 9.9 - - + +
286A PRO* 3.5 11.5 - - + +
287A PHE* 2.6 47.0 + - + -
289A VAL* 5.1 5.8 - - + -
386A ILE 3.9 0.3 - - - +
387A SER* 3.3 5.5 - - - -
388A MET* 3.1 49.9 + - + +
390A PHE* 3.6 34.8 - + - -
428A SER* 4.2 8.1 - - - -
429A GLY 3.6 1.8 + - - -
430A ILE* 1.3 73.8 - - - +
432A GLU* 1.3 61.1 + - - +
433A THR* 5.1 2.5 + - - -
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Residues in contact with GLU 432 (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 LEU* 3.0 12.6 + - - +
184A LEU* 3.5 19.1 - - + +
185A MET* 2.9 25.3 + - - +
385A PRO* 3.7 31.7 - - + +
386A ILE 3.5 3.6 - - - -
387A SER* 4.0 15.4 - - - -
430A ILE* 3.9 21.5 - - + +
431A TYR* 1.3 76.5 - - - +
433A THR* 1.3 65.6 + - - +
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Residues in contact with THR 433 (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 LEU* 5.1 6.1 - - - +
185A MET* 3.7 25.0 - - + +
186A SER 4.6 2.5 - - - +
187A PRO* 5.8 0.4 - - + +
288A ARG* 5.1 0.9 - - - +
289A VAL* 3.6 50.4 + - + +
291A PRO* 4.4 10.3 - - + -
385A PRO* 3.3 2.4 - - - +
386A ILE* 2.7 42.9 + - - +
431A TYR* 5.1 3.1 + - - -
432A GLU* 1.3 78.3 + - - +
434A ARG* 1.3 70.4 + - - +
435A CYS 3.6 0.7 + - - -
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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