Contacts of the strand formed by residues 317 - 324 (chain B) in PDB entry 1EKF
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 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B PHE* 4.2 4.9 - - - -
274B LEU* 4.7 5.2 - - + -
309B PHE* 3.3 35.2 - - + -
310B GLY 3.4 2.5 - - - -
315B CYS* 4.3 2.0 - - - -
316B GLN* 1.3 88.7 - - + +
318B CYS* 1.3 58.0 + - - +
319B PRO* 3.7 6.1 - - - +
342B ILE* 3.7 25.3 - - + +
345B PHE* 4.0 18.2 - - + -
346B GLN* 3.1 46.5 + - + +
349B LEU* 4.4 9.4 - - + -
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Residues in contact with CYS 318 (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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173B TYR* 5.7 2.5 - - - -
174B PHE* 4.6 5.6 - - - -
180B THR 4.8 0.4 - - - -
182B VAL* 3.8 33.9 - - - -
224B GLN* 5.1 1.3 - - - -
241B MET* 3.9 20.9 - - + -
309B PHE* 3.0 6.0 - - - -
310B GLY 2.8 38.3 + - - +
315B CYS* 3.1 28.5 - - - -
317B VAL* 1.3 72.4 - - - +
319B PRO* 1.3 73.0 - - - +
320B VAL* 4.0 1.9 - - - +
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Residues in contact with PRO 319 (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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174B PHE* 4.2 3.4 - - + -
179B VAL* 3.6 28.0 - - + +
180B THR 4.0 15.3 - - - +
181B PRO* 3.2 9.3 - - + +
182B VAL* 2.9 27.2 + - - +
308B VAL 3.9 0.4 - - - +
317B VAL 3.7 7.2 - - - +
318B CYS* 1.3 85.7 - - + +
320B VAL* 1.3 60.6 + - - +
334B THR* 4.0 2.9 - - + -
335B MET* 3.8 26.7 - - - -
339B PRO* 5.8 0.7 - - + -
342B ILE* 3.7 29.8 - - + -
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Residues in contact with VAL 320 (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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181B PRO* 4.2 1.1 - - - -
182B VAL* 3.5 18.6 - - + +
184B LEU* 3.7 33.9 - - + -
238B VAL* 5.2 4.7 - - + -
308B VAL* 2.9 28.0 + - + +
309B PHE* 4.1 9.4 - - - -
310B GLY* 4.5 2.0 - - - +
318B CYS 4.0 7.0 - - - +
319B PRO* 1.3 79.4 - - - +
321B HIS* 1.3 64.0 + - - +
322B ARG 4.0 12.8 - - - +
323B ILE* 4.0 11.4 - - + -
332B ILE* 3.5 11.8 - - + +
334B THR* 2.7 28.1 + - - -
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Residues in contact with HIS 321 (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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181B PRO* 3.4 37.1 - - + +
182B VAL 3.2 29.1 + - - -
183B SER* 3.8 10.1 - - - -
223B GLU* 4.1 5.2 - - - -
320B VAL* 1.3 73.5 - - - +
322B ARG* 1.3 77.0 + - + +
331B HIS* 3.5 20.7 + + + -
332B ILE* 2.7 39.5 + - - +
334B THR* 5.2 0.2 - - - -
335B MET* 5.0 7.2 - - + -
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Residues in contact with ARG 322 (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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182B VAL 3.9 0.8 + - - -
183B SER* 3.2 23.9 + - - -
184B LEU 2.8 24.3 + - - -
220B ARG 5.3 0.8 + - - -
221B GLY* 2.9 27.1 + - - -
222B CYS* 4.3 14.3 - - - -
320B VAL* 3.8 2.7 - - - +
321B HIS* 1.3 102.2 + - + +
323B ILE* 1.3 73.0 + - - +
324B LEU* 4.4 6.2 - - - +
329B ASN* 2.8 50.2 + - + +
330B LEU 3.3 11.2 - - - +
331B HIS* 5.2 1.8 - - - +
332B ILE* 3.8 1.0 - - - +
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Residues in contact with ILE 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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184B LEU* 3.4 16.2 - - + +
186B ALA* 3.9 25.8 - - + -
226B LEU* 4.0 17.3 - - + -
235B LEU* 5.2 2.0 - - + -
243B ILE* 5.9 0.4 - - + -
293B MET* 4.7 4.5 - - + -
296B LEU* 4.0 18.4 - - + -
308B VAL* 5.1 9.4 - - + -
320B VAL* 4.0 15.9 - - + -
322B ARG* 1.3 81.9 - - - +
324B LEU* 1.3 60.8 + - - +
325B TYR 3.3 4.4 + - - +
330B LEU* 2.8 55.8 + - + +
332B ILE* 3.9 20.4 - - + -
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Residues in contact with LEU 324 (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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184B LEU 2.7 15.9 + - - +
185B LEU* 3.6 11.2 - - + +
186B ALA 2.9 23.1 + - - +
220B ARG* 3.7 47.8 - - - +
222B CYS* 3.8 17.3 - - - -
322B ARG* 4.2 5.0 - - - +
323B ILE* 1.3 69.6 - - - +
325B TYR* 1.3 63.0 + - - +
327B ASP* 3.6 35.9 - - - +
328B ARG 3.7 5.2 - - - -
329B ASN* 3.6 25.6 - - - +
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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