Contacts of the strand formed by residues 310 - 318 (chain C) in PDB entry 4LCC
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 THR 310 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301C HIS* 3.3 7.3 - - - +
302C LYS 3.3 27.0 + - - -
309C THR* 1.3 87.9 + - - +
311C LEU* 1.3 69.3 + - - +
312C TYR* 3.5 37.9 + - + +
356C SER* 4.2 13.7 - - - +
357C VAL 3.6 9.4 - - - +
358C GLU* 4.5 9.0 - - + +
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Residues in contact with LEU 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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300C ASN 3.5 1.1 - - - +
301C HIS* 3.6 12.3 - - + -
309C THR 5.3 5.2 - - - +
310C THR* 1.3 86.8 - - - +
312C TYR* 1.3 61.5 + - - +
327C TRP* 3.3 24.9 + - + -
356C SER* 3.1 7.5 - - - -
357C VAL* 2.9 39.3 + - + +
359C LEU* 5.4 8.5 - - + -
367C TYR* 4.0 35.4 - - + -
383C PHE* 3.4 41.3 - - + -
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Residues in contact with TYR 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ASP* 4.8 13.6 + - - -
298C ARG 4.5 0.2 - - - -
299C VAL* 3.3 12.1 - - - +
300C ASN* 2.8 56.7 + - + +
301C HIS* 4.4 0.9 - - - -
302C LYS* 3.9 28.4 - - + +
310C THR* 3.5 32.2 - - + +
311C LEU* 1.3 75.9 - - - +
313C CYS* 1.3 61.2 + - - +
314C ARG* 4.3 6.7 - - + +
327C TRP* 3.6 1.6 - - - -
354C TRP* 4.9 13.9 - + + -
355C VAL 4.0 2.0 - - - -
356C SER* 4.0 15.7 - - - -
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Residues in contact with CYS 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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297C VAL* 3.6 21.3 - - - -
298C ARG 3.6 2.9 - - - -
299C VAL* 4.7 1.3 - - + +
312C TYR* 1.3 76.0 - - - +
314C ARG* 1.3 60.7 + - - +
325C ILE* 4.2 10.5 - - + +
327C TRP* 3.8 9.6 - - + +
354C TRP* 3.0 26.7 - - - +
355C VAL 3.1 19.9 + - - +
369C CYS* 2.0 47.1 - - - -
371C VAL* 4.6 2.5 - - - -
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Residues in contact with ARG 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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8C GLN* 4.3 3.2 + - - +
9C VAL 4.4 5.5 + - - -
10C TYR* 4.0 16.9 - - - +
296C LYS 3.8 1.7 - - - +
297C VAL* 3.3 6.2 - - - +
298C ARG* 2.9 38.2 + - + +
312C TYR* 4.3 5.4 - - + -
313C CYS* 1.3 76.2 - - - +
315C ALA* 1.3 60.1 + - - +
316C TYR* 3.5 37.4 + - + +
344C LEU* 3.6 17.2 - - - +
352C GLN* 2.9 36.4 + - - +
353C THR 3.5 10.6 + - - -
354C TRP* 3.3 36.1 - - + +
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Residues in contact with ALA 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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295C PRO* 3.8 21.1 - - + -
296C LYS 4.0 3.4 - - - -
297C VAL* 4.5 8.3 - - + +
313C CYS 4.3 0.2 + - - -
314C ARG* 1.3 72.5 - - - +
316C TYR* 1.3 61.4 + - - +
318C PHE* 3.3 13.3 - - + -
323C ILE* 4.3 3.6 - - + -
325C ILE* 3.7 25.1 - - + -
352C GLN* 3.0 27.6 - - - +
353C THR 3.0 9.6 + - - +
371C VAL* 4.9 0.4 - - + -
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Residues in contact with TYR 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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11C SER* 4.1 12.5 + - - -
12C ARG 5.0 2.7 - - - +
13C HIS* 4.0 21.8 - - - -
14C PRO* 4.2 26.5 - - + +
294C PRO 4.1 0.2 - - - +
295C PRO* 3.4 3.8 - - - +
296C LYS* 3.3 53.0 + - + +
298C ARG* 4.0 21.9 - - + +
314C ARG* 3.5 35.8 - - + +
315C ALA* 1.3 73.6 - - - +
317C GLY* 1.3 67.4 + - - +
318C PHE 3.6 1.8 - - - -
352C GLN* 3.3 37.9 - - - -
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Residues in contact with GLY 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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12C ARG 5.1 2.4 + - - -
293C GLU* 4.1 12.8 - - - +
294C PRO 3.3 13.5 - - - +
296C LYS* 5.8 0.2 - - - -
316C TYR* 1.3 73.6 - - - +
318C PHE* 1.3 58.1 + - - +
346C SER* 4.7 6.5 + - - -
348C ASP* 5.8 0.2 - - - -
350C THR* 3.8 24.2 - - - +
351C TYR 3.2 11.7 + - - -
352C GLN* 4.4 2.2 - - - +
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Residues in contact with PHE 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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293C GLU 3.3 12.3 - - - +
295C PRO* 3.7 24.0 - - + -
315C ALA* 3.3 23.1 - - + -
317C GLY* 1.3 78.5 - - - +
319C TYR* 1.3 65.2 + - - +
320C PRO 3.8 3.1 - - - -
321C PRO 3.7 13.7 - - - -
323C ILE* 3.5 37.7 - - + -
343C ILE* 4.7 0.7 - - + -
350C THR* 3.5 2.0 - - - -
351C TYR* 2.9 62.8 + - + -
352C GLN* 3.4 5.4 - - - -
353C THR* 3.5 27.6 - - + -
373C HIS* 3.7 20.2 - + + +
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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