Contacts of the strand formed by residues 307 - 317 (chain C) in PDB entry 1XKH
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 307 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300C PRO* 3.8 2.9 - - - +
301C LEU* 3.1 35.9 + - + -
302C THR* 3.3 34.8 + - + +
305C GLY 2.6 9.5 + - - +
306C ASN* 1.3 79.2 - - + +
308C ARG* 1.3 65.0 + - - +
336C LEU* 5.0 6.5 - - + -
337C GLU 3.2 15.0 - - - +
338C PHE* 3.9 27.4 - - + -
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Residues in contact with ARG 308 (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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273C PRO* 4.1 8.9 - - + +
274C THR 4.6 6.5 - - - +
275C HIS* 2.9 53.5 + - - +
299C GLY 3.4 12.6 - - - +
300C PRO* 4.3 10.3 - - + -
301C LEU* 4.6 3.6 - - - -
305C GLY* 3.4 16.1 + - - +
306C ASN 4.7 0.2 + - - -
307C VAL* 1.3 78.2 - - - +
309C GLY* 1.3 58.1 + - - +
336C LEU* 3.2 3.5 - - - +
337C GLU* 2.7 67.0 + - + +
339C ASP* 2.5 37.8 + - - +
345C MSE 3.3 28.7 - - - +
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Residues in contact with GLY 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C PRO* 3.8 4.7 - - - +
297C VAL 4.2 0.3 - - - +
298C SER* 3.4 1.9 - - - -
299C GLY 2.9 32.7 + - - +
301C LEU* 4.1 15.9 - - - +
308C ARG* 1.3 75.5 - - - +
310C ARG* 1.3 60.9 + - - -
335C ILE 3.4 7.9 - - - -
336C LEU* 3.8 11.4 - - - -
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Residues in contact with ARG 310 (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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142C GLU* 3.1 30.1 + - - -
271C LYS* 2.4 60.1 - - - +
272C LYS 3.4 14.8 + - - +
273C PRO* 3.8 9.5 - - + +
274C THR* 5.4 3.2 - - - +
296C ASP* 2.4 38.0 + - - +
297C VAL 3.3 6.3 - - - +
298C SER* 3.4 27.9 - - - +
309C GLY* 1.3 74.2 - - - -
311C ALA* 1.3 64.1 + - - +
312C VAL* 5.3 1.7 - - + +
333C TYR* 4.7 3.5 - - + -
334C GLY* 3.5 1.7 - - - -
335C ILE* 2.7 55.4 + - + +
336C LEU* 4.7 2.5 - - - +
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Residues in contact with ALA 311 (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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295C LEU* 3.7 1.9 - - - +
297C VAL* 2.8 38.2 + - + +
310C ARG* 1.3 75.8 - - - +
312C VAL* 1.3 61.6 + - - +
333C TYR* 3.4 10.1 - - - +
334C GLY* 4.6 4.3 - - - -
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Residues in contact with VAL 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ALA* 3.4 22.0 - - + +
242C ILE* 3.7 16.5 - - + +
271C LYS* 5.0 3.1 - - + -
294C GLU* 4.8 3.6 - - - +
295C LEU 3.0 24.9 - - - +
296C ASP* 3.9 18.8 - - + +
310C ARG* 5.7 1.1 - - + +
311C ALA* 1.3 75.4 - - - +
313C ALA* 1.3 71.1 + - - +
331C VAL 4.7 0.2 - - - -
332C TYR 3.6 1.0 - - - -
333C TYR* 3.0 57.6 + - + +
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Residues in contact with ALA 313 (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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294C GLU* 3.3 1.6 - - - -
295C LEU* 2.9 31.6 + - + +
312C VAL* 1.3 80.4 - - - +
314C ALA* 1.3 60.4 + - - +
315C TYR* 5.2 6.7 - - + -
331C VAL* 2.9 19.1 - - - +
332C TYR* 3.4 26.0 - - + -
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Residues in contact with ALA 314 (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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239C ASP* 4.4 2.2 - - - +
241C ALA* 4.0 11.9 - - + -
292C ARG* 4.2 10.8 - - - +
293C SER 3.1 7.6 - - - +
294C GLU* 3.3 23.3 - - + -
313C ALA* 1.3 75.1 - - - +
315C TYR* 1.3 70.6 + - - +
330C SER* 3.5 4.0 - - - -
331C VAL* 2.9 44.7 + - + +
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Residues in contact with TYR 315 (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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292C ARG* 3.1 4.0 - - - +
293C SER* 2.7 54.8 + - - +
313C ALA* 5.2 5.2 - - + -
314C ALA* 1.3 81.4 - - - +
316C GLN* 1.3 59.4 + - - +
329C THR 3.9 3.8 - - - +
330C SER* 3.7 17.9 - - - -
332C TYR* 3.1 46.9 + + - -
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Residues in contact with GLN 316 (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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183C ASN* 4.0 17.7 - - - +
184C ASN* 5.4 4.9 + - - +
239C ASP* 3.7 7.9 - - - +
290C ASN* 3.2 25.9 + - - +
291C TYR 3.2 10.8 - - - +
292C ARG* 3.0 38.5 + - + +
315C TYR* 1.3 75.8 - - - +
317C ASP* 1.3 65.2 + - - +
318C LYS* 4.7 14.7 + - + +
327C ARG 4.3 0.7 - - - +
328C LYS* 3.3 3.2 - - - +
329C THR* 3.0 51.5 + - + +
808C MSE 5.1 1.2 - - - -
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Residues in contact with ASP 317 (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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289C ASP 3.1 7.0 - - - +
291C TYR* 2.8 38.0 + - + +
316C GLN* 1.3 73.4 - - - +
318C LYS* 1.3 73.3 + - - +
319C HIS* 4.4 10.0 + - - -
326C GLU* 5.2 2.8 - - - +
327C ARG 3.9 6.9 - - - +
328C LYS* 4.0 23.3 + - + +
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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