Contacts of the strand formed by residues 301 - 306 (chain B) in PDB entry 4CH9
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 LYS 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B PRO* 1.3 77.8 - - + +
302B VAL* 1.3 68.8 + - - +
321B ASP* 4.8 1.9 - - - +
322B PHE* 3.3 29.2 + - + +
323B GLU* 5.1 2.7 + - - +
535B VAL* 3.7 21.8 - - + +
536B ASN* 2.8 31.8 + - - +
582B VAL* 3.9 14.1 - - + -
583B ILE 3.2 11.9 - - - +
584B HIS* 3.8 30.7 - - + +
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LYS* 1.3 80.8 - - - +
303B MET* 1.3 60.7 + - - +
304B ILE* 3.7 6.0 + - + -
319B CYS* 3.4 28.5 - - - -
320B TYR 3.3 14.4 - - - +
321B ASP* 4.0 11.7 - - + +
322B PHE* 3.9 5.6 - - - -
582B VAL* 3.4 4.7 - - - +
583B ILE* 2.9 55.6 + - + +
585B LYS* 4.0 35.4 - - + -
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Residues in contact with MET 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B VAL* 1.3 73.6 - - - +
304B ILE* 1.3 63.9 + - - +
305B VAL* 4.0 4.6 + - + +
318B GLU 3.8 0.2 - - - +
319B CYS* 3.2 3.8 - - - -
320B TYR* 2.7 51.3 + - + +
322B PHE* 3.8 20.6 - - + -
327B TRP* 4.0 24.0 - - + -
533B CYS* 3.6 24.5 - - - -
540B TYR* 4.1 11.0 - - + -
542B VAL* 3.8 26.5 - - + -
554B VAL* 4.3 12.8 - - + -
567B LEU* 4.7 1.3 - - + -
580B VAL* 3.6 17.7 - - + -
581B ALA 3.5 4.5 - - - +
582B VAL* 4.5 2.0 - - + +
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B VAL* 3.7 10.3 - - + -
303B MET* 1.3 73.6 - - - +
305B VAL* 1.3 64.7 + - - +
306B VAL* 4.0 12.7 - - + +
317B VAL* 3.6 26.2 - - + -
318B GLU 3.4 2.0 - - - +
319B CYS* 3.6 35.7 - - + -
330B ILE* 4.0 14.8 - - + -
349B VAL* 4.9 11.7 - - + -
367B TYR* 5.7 2.5 - - + -
374B TRP* 5.4 2.2 - - + -
579B GLY 3.8 0.5 - - - +
580B VAL* 3.2 7.8 - - - +
581B ALA* 2.7 40.8 + - + +
583B ILE* 3.7 32.1 - - + -
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET* 4.6 8.5 - - + +
304B ILE* 1.3 77.7 - - - +
306B VAL* 1.3 63.3 + - - +
317B VAL* 3.3 4.9 - - - -
318B GLU* 2.8 39.6 + - + +
327B TRP* 3.8 27.4 - - + -
542B VAL* 4.0 25.6 - - + -
571B MET* 4.5 2.7 - - - -
575B ARG* 3.7 33.5 + - - +
578B ALA* 3.7 12.6 - - + -
579B GLY 3.5 4.5 - - - +
580B VAL* 4.1 6.1 - - + -
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ILE* 4.0 20.6 - - + +
305B VAL* 1.3 75.1 - - - +
307B GLY* 1.3 68.6 + - - +
308B GLY 3.7 0.3 + - - -
317B VAL* 4.3 6.7 - - + -
333B LEU* 3.9 31.9 - - + -
338B CYS* 5.9 0.3 - - - -
340B ALA* 5.8 6.3 - - + +
342B VAL* 3.8 32.2 - - + +
349B VAL* 4.7 1.6 - - + -
351B ALA* 4.2 5.6 - - + -
374B TRP* 4.2 19.3 - - + -
577B TYR 4.8 0.2 - - - +
578B ALA* 3.7 0.9 - - - -
579B GLY 2.8 33.0 + - - +
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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