Contacts of the strand formed by residues 312 - 320 (chain C) in PDB entry 1XPU
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 312 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170C ARG* 3.4 17.4 - - - +
171C GLY 3.9 13.9 + - - -
254C VAL* 3.4 11.9 - - - +
258C LYS 3.2 6.8 + - - +
259C ASP* 2.8 27.4 + - - +
260C VAL 2.9 26.6 + - - +
305C ARG 3.6 12.3 - - - -
306C ASN* 3.9 11.2 - - - -
307C VAL 4.2 1.1 - - - +
311C GLY* 1.3 75.7 - - - -
313C LEU* 1.3 59.8 + - - +
314C THR* 4.7 2.8 - - - +
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Residues in contact with LEU 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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132C LEU* 4.3 17.5 - - + -
171C GLY* 3.2 5.2 - - - -
247C ILE* 4.3 9.6 - - + -
250C ALA* 4.0 13.2 - - + -
251C LYS* 4.7 7.0 - - + -
254C VAL* 3.9 11.3 - - + +
260C VAL* 3.6 11.0 - - + +
262C ILE* 3.8 30.3 - - + -
303C ALA* 3.4 37.5 - - + +
304C ALA* 3.4 6.8 - - - +
305C ARG* 2.7 43.3 + - + +
312C SER* 1.3 74.5 - - - +
314C THR* 1.3 62.6 + - - +
315C ILE* 4.4 4.7 - - + -
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Residues in contact with THR 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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145C LEU* 4.6 4.5 - - + +
168C ILE* 5.1 1.6 - - - +
169C GLY 4.4 3.1 + - - +
170C ARG* 4.4 7.0 - - + -
171C GLY 3.5 14.6 - - - +
172C GLN* 3.3 32.2 + - - +
259C ASP* 5.8 0.9 - - + -
260C VAL 3.0 18.6 + - - +
261C ILE* 3.4 28.5 - - + +
262C ILE* 2.7 32.7 + - - +
312C SER* 4.7 4.0 - - - +
313C LEU* 1.3 75.0 - - - +
315C ILE* 1.3 57.0 + - - +
316C ILE* 4.2 9.4 - - - +
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Residues in contact with ILE 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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172C GLN 3.0 7.3 + - - +
173C ARG* 3.6 2.1 - - - -
174C GLY 2.8 26.0 + - - +
247C ILE* 3.7 19.5 - - + -
262C ILE* 3.2 23.8 - - + +
264C LEU* 4.4 4.3 - - + -
300C PHE* 3.2 46.4 - - + +
301C PHE* 4.0 21.4 - - + +
304C ALA* 3.7 25.2 - - + +
313C LEU* 4.4 4.7 - - + -
314C THR* 1.3 76.9 - - - +
316C ILE* 1.3 64.5 + - - +
317C ALA* 4.3 9.9 - - + +
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Residues in contact with ILE 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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168C ILE* 4.3 32.3 - - + -
172C GLN* 4.3 5.8 - - + -
174C GLY* 3.3 23.6 - - - +
176C ILE* 3.7 32.5 - - + -
188C LEU* 4.6 6.8 - - + +
191C ILE* 5.7 6.1 - - + -
261C ILE* 5.2 3.8 - - + -
262C ILE 2.9 7.5 + - - +
263C LEU* 3.7 28.6 - - + +
264C LEU 3.0 24.3 + - - +
314C THR* 4.2 14.1 - - - +
315C ILE* 1.3 79.0 - - - +
317C ALA* 1.3 58.7 + - - +
341C MET* 4.9 3.4 - - + -
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Residues in contact with ALA 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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174C GLY 2.8 9.1 + - - -
175C LEU* 3.2 9.6 - - + +
176C ILE 2.8 23.0 + - - -
264C LEU* 3.1 34.8 - - + +
267C ILE* 4.0 12.6 - - + -
301C PHE* 3.6 24.7 - - + -
315C ILE* 3.8 1.5 - - + -
316C ILE* 1.3 73.4 - - - +
318C THR* 1.3 63.1 + - - +
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Residues in contact with THR 318 (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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176C ILE* 3.1 27.8 - - + -
184C LYS* 3.8 24.0 - - + +
188C LEU* 3.8 26.0 - - + -
264C LEU 3.1 4.9 + - - +
265C ASP* 2.7 18.0 + - - +
266C SER* 2.5 32.7 + - - -
267C ILE* 2.9 28.1 + - - +
317C ALA* 1.3 74.9 - - - +
319C ALA* 1.3 59.7 + - - +
320C LEU* 4.0 1.8 - - - +
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Residues in contact with ALA 319 (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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175C LEU* 4.0 19.3 - - + -
176C ILE 2.8 11.4 + - - +
177C VAL* 3.8 2.1 - - - +
178C ALA* 3.2 23.7 + - - -
267C ILE* 4.3 3.8 - - + -
268C THR* 3.9 13.9 - - + -
317C ALA 3.9 0.8 + - - -
318C THR* 1.3 72.5 - - - +
320C LEU* 1.3 65.5 + - - +
321C ILE* 3.4 3.0 + - - +
332C TYR* 3.7 32.3 - - + -
335C PHE* 6.3 0.9 - - + -
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Residues in contact with LEU 320 (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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178C ALA 3.7 4.3 - - - +
184C LYS* 3.7 27.1 - - + +
266C SER* 3.7 24.0 - - - -
268C THR* 3.2 29.2 + - - +
269C ARG* 3.8 18.6 - - + +
318C THR* 4.0 8.5 - - - +
319C ALA* 1.3 71.4 - - - +
321C ILE* 1.3 61.7 + - - +
323C THR* 3.9 15.8 + - - +
328C ASP* 3.9 16.3 - - - +
332C TYR* 5.3 0.3 - - - +
3701C FPD 3.5 49.6 - - + +
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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