Contacts of the strand formed by residues 318 - 323 (chain B) in PDB entry 1K3B
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 SER 318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B LEU* 3.8 17.2 - - - +
283B ALA 2.9 27.6 + - - -
284B GLY* 4.0 7.4 - - - -
287B ALA* 3.1 19.4 + - - +
288B GLN* 3.2 25.0 + - - +
317B TYR* 1.3 75.0 - - - +
319B SER* 1.3 63.5 + - - +
320B GLU 3.2 11.0 - - - -
321B TYR* 5.1 0.2 - - - -
433C ALA* 4.2 0.6 - - - +
434C THR 3.1 11.4 + - - -
435C PRO* 4.2 0.3 - - - +
436C ILE* 4.6 1.6 - - - -
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Residues in contact with SER 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLN* 3.5 12.2 + - - +
318B SER* 1.3 72.3 - - - +
320B GLU* 1.3 63.6 + - - +
434C THR* 2.8 29.9 + - - +
436C ILE* 3.7 29.5 - - - +
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Residues in contact with GLU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLN* 4.3 1.8 - - - +
318B SER* 3.2 3.9 + - - -
319B SER* 1.3 85.9 + - - +
321B TYR* 1.3 90.6 + - - +
322B HIS* 3.0 37.0 + - - +
432C ALA 4.7 0.9 - - - +
433C ALA* 3.2 4.2 - - - +
434C THR* 2.8 44.3 + - - +
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Residues in contact with TYR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 2.7 39.7 + - - -
76A LYS* 3.4 22.5 + - - +
280B TYR* 3.8 26.3 + + - -
284B GLY* 3.4 40.8 - - - -
285B LYS* 3.8 22.0 + - - +
288B GLN* 3.5 32.3 + - + -
289B ASP* 5.3 0.2 + - - -
318B SER 5.1 0.4 - - - -
320B GLU* 1.3 92.8 - - - +
322B HIS* 1.3 64.8 + - - +
431C VAL* 5.5 2.5 - - + -
432C ALA 3.2 13.9 - - - +
433C ALA* 3.9 1.6 - - + -
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Residues in contact with HIS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B TYR* 4.1 14.5 - - - -
320B GLU* 3.0 35.3 + - - +
321B TYR* 1.3 76.1 - - - +
323B TYR* 1.3 80.1 + - - +
324B VAL* 4.0 11.6 - - + -
325B GLY 5.2 0.9 - - - -
326B GLY* 4.8 10.2 + - - +
339B GLU* 3.9 20.4 + - - -
431C VAL* 3.8 1.6 - - - +
432C ALA* 3.0 46.1 + - + +
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Residues in contact with TYR 323 (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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61A THR* 3.4 19.5 - - + -
62A ILE 3.5 19.7 - - - -
63A ILE* 3.4 26.1 - - - +
64A TYR* 3.7 5.0 + - - +
280B TYR* 3.5 30.8 - + + -
322B HIS* 1.3 79.6 + - - +
324B VAL* 1.3 61.3 + - - +
326B GLY* 2.9 25.4 + - - -
327B PHE* 3.6 20.2 - - - +
328B TYR* 3.5 13.5 - + + -
500B CL 3.3 13.9 - - + +
429C ILE* 3.3 31.5 - - + +
430C ALA 3.7 7.6 - - - +
431C VAL* 3.4 24.9 - - + -
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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
------------------------------------------------------------
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