Contacts of the strand formed by residues 374 - 380 (chain C) in PDB entry 1K9I
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 PHE 374 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271C SER* 3.5 24.2 - - - +
272C ASN 3.1 24.5 - - - -
273C SER 3.7 6.7 - - - -
274C GLN* 3.2 37.0 - - + -
312C ARG* 3.3 58.6 - - + -
313C PHE 3.1 15.4 + - - +
314C THR* 3.0 15.0 - - + +
315C TRP* 2.8 23.6 + - - +
373C LYS* 1.3 79.8 - - - +
375C TRP* 1.3 61.4 + - - +
310F SER* 6.3 0.2 - - - -
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Residues in contact with TRP 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C PHE* 4.9 2.4 - + - -
270C MET* 3.9 0.2 - - - -
271C SER* 2.8 61.0 + - - -
273C SER* 2.7 43.3 - - - -
275C ARG* 3.0 31.6 - - + -
280C SER* 3.8 31.4 - - - +
283C ALA* 4.0 14.8 - - + +
284C CYS* 3.7 8.8 - - - -
291C LEU* 4.0 11.0 - - + -
314C THR* 3.3 5.9 - - - +
315C TRP* 4.2 6.7 - - + +
373C LYS 3.9 6.3 - - - -
374C PHE* 1.3 75.7 - - - +
376C ILE* 1.3 71.2 + - - +
377C CYS* 3.2 33.1 - - - -
258F TRP* 4.8 2.0 - + - -
259F GLU* 3.3 21.3 - - + -
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Residues in contact with ILE 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C TYR* 4.5 7.2 - - + -
269C PHE 3.1 18.2 - - - +
270C MET* 4.2 24.5 - - + -
291C LEU* 3.6 7.0 - - - +
292C VAL* 2.9 41.4 + - + +
303C LEU* 4.5 17.9 - - + +
306C GLN* 6.0 2.0 - - + -
307C SER* 4.0 17.3 - - - +
314C THR* 3.5 20.5 - - + +
315C TRP 4.0 4.0 + - - -
359C PHE* 4.3 15.5 - - + -
375C TRP* 1.3 87.6 - - - +
377C CYS* 1.3 67.7 + - - +
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Residues in contact with CYS 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C TRP* 4.0 13.6 - - + -
267C CYS 3.8 0.2 - - - +
268C TYR* 3.3 5.7 - - - -
269C PHE* 2.9 34.2 + - + -
284C CYS* 2.0 54.3 - - - -
289C ALA* 3.8 13.7 - - + -
290C GLN 3.6 0.2 - - - -
375C TRP* 3.2 17.9 - - - -
376C ILE* 1.3 77.0 - - - +
378C LYS* 1.3 61.6 + - - +
258F TRP* 4.1 15.3 - - - -
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Residues in contact with LYS 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C ASN* 3.8 24.5 - - + +
267C CYS 3.4 5.6 - - - +
268C TYR* 3.5 27.6 - - + -
289C ALA* 3.6 1.7 - - - -
290C GLN* 2.9 37.6 + - - +
292C VAL* 4.1 11.2 - - + -
293C VAL* 3.0 26.3 + - + +
295C LYS* 4.5 13.1 - - - +
299C GLU* 2.7 36.7 + - - +
377C CYS* 1.3 76.8 - - - +
379C LYS* 1.3 66.7 + - - +
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Residues in contact with LYS 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C PRO* 3.7 33.6 - - - +
260C TRP* 4.3 16.4 - - + -
266C ASN* 3.5 5.3 - - - -
267C CYS* 2.6 41.7 + - + +
287C VAL* 3.3 22.4 + - - +
288C GLY* 3.5 26.4 + - - +
289C ALA* 4.0 5.2 - - + -
378C LYS* 1.3 79.4 - - - +
380C SER* 1.3 67.3 + - - +
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Residues in contact with SER 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C GLY 3.6 3.4 - - - -
266C ASN* 3.3 18.8 + - - -
267C CYS* 4.4 2.1 - - - -
379C LYS* 1.3 89.6 - - - +
381C ALA* 1.3 67.9 + - - +
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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
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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