Contacts of the strand formed by residues 307 - 315 (chain C) in PDB entry 1SMK
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 307 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C VAL* 3.7 20.6 - - + -
169C PRO* 3.6 33.0 - - + -
172C ALA* 3.5 26.2 - - + -
173C GLU* 5.8 2.0 - - - -
176C LYS* 6.1 2.9 - - - -
181C TYR* 3.9 8.7 - - - -
186C LEU* 4.9 2.9 - - + -
297C PHE* 3.4 23.6 - + + -
298C VAL 3.3 6.1 - - - +
299C SER* 3.5 36.8 - - - -
300C SER* 4.5 0.9 - - - +
305C LEU* 3.6 10.2 - - - +
306C PRO* 1.3 98.7 - - + +
308C PHE* 1.3 76.0 + - - +
343C LEU* 3.7 7.3 - - - +
347C ILE* 3.8 8.4 - - + +
351C VAL* 5.1 5.2 - - + -
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Residues in contact with PHE 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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217C VAL* 4.2 0.9 - - + -
218C GLY* 3.3 29.6 - - - -
296C ALA 3.4 1.9 - - - +
297C PHE* 3.6 8.8 - - - -
298C VAL* 2.9 30.6 + - - +
300C SER* 3.8 15.5 + - - +
302C VAL* 4.5 3.1 - - + -
303C THR* 3.6 37.0 - - + +
305C LEU* 4.2 9.9 - - + +
307C PHE* 1.3 80.5 - - - +
309C ALA* 1.3 77.5 + - - +
310C SER* 3.8 2.6 + - - +
325C LEU* 3.7 26.0 - - + -
336C LEU* 3.6 24.9 - - + -
339C ALA* 5.1 2.2 - - + -
340C LYS* 4.2 11.2 - - + -
343C LEU* 3.5 22.0 - - + -
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Residues in contact with ALA 309 (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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190C THR* 4.2 15.0 - - + +
216C VAL 4.3 5.6 - - - +
217C VAL* 3.1 16.5 - - - +
218C GLY 2.7 46.6 + - - +
219C GLY* 4.3 1.3 - - - +
296C ALA 2.9 20.0 - - - +
297C PHE* 3.5 8.0 - - + +
308C PHE* 1.3 75.3 - - - +
310C SER* 1.3 62.4 + - - +
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Residues in contact with SER 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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216C VAL 4.5 1.1 + - - -
217C VAL* 4.2 10.8 - - - -
295C CYS* 3.1 7.0 - - - -
296C ALA 3.0 25.4 + - - +
300C SER* 5.0 0.7 + - - -
302C VAL* 4.5 5.4 - - - +
308C PHE* 4.5 4.5 + - - -
309C ALA* 1.3 76.5 - - - +
311C LYS* 1.3 64.7 + - - +
312C VAL* 3.5 6.1 + - - +
322C VAL* 3.4 20.8 - - - +
323C TYR 3.4 20.5 + - - -
324C SER 4.8 1.8 - - - -
325C LEU* 3.9 17.7 - - - -
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Residues in contact with LYS 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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213C ASP* 2.9 34.2 + - - -
215C PRO* 3.6 33.3 - - + +
217C VAL* 5.3 2.1 - - + +
231C GLN* 6.1 0.4 - - - +
233C LYS* 5.1 6.1 - - - +
293C ILE* 3.9 22.7 + - + +
294C GLU* 3.6 7.5 - - - +
295C CYS* 3.8 17.0 - - - +
310C SER* 1.3 76.8 + - - +
312C VAL* 1.3 62.3 + - - +
323C TYR* 2.8 49.7 + - + +
324C SER 5.0 5.4 + - - +
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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
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187C LEU* 4.8 0.4 - - + -
278C PHE* 5.6 0.2 - - + -
292C VAL 3.7 0.7 - - - +
293C ILE* 3.3 2.6 - - - -
294C GLU* 2.8 35.6 + - + +
296C ALA* 4.6 11.7 - - + +
298C VAL* 4.2 30.3 - - + -
310C SER 3.6 11.0 - - - +
311C LYS* 1.3 80.7 - - - +
313C ARG* 1.3 60.5 + - - +
314C LEU* 3.8 28.3 + - + +
319C ILE* 4.1 11.2 - - + -
321C GLU 3.3 11.2 - - - +
322C VAL* 4.3 11.2 - - + -
323C TYR* 4.3 5.6 - - - -
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Residues in contact with ARG 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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289C ASP 4.7 6.1 + - - -
290C ALA* 4.9 2.8 - - - +
291C GLY* 4.4 22.8 - - - +
292C VAL 3.3 12.8 - - - +
293C ILE* 4.3 6.5 - - + -
312C VAL* 1.3 73.6 - - - +
314C LEU* 1.3 74.8 + - - +
315C GLY* 4.9 2.2 - - - -
319C ILE* 3.6 4.5 - - - -
320C GLU* 2.9 51.4 + - - +
321C GLU* 2.9 23.0 + - + +
323C TYR* 3.3 31.2 + - + +
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Residues in contact with LEU 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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187C LEU* 3.7 26.9 - - + -
278C PHE* 4.3 12.6 - - + -
281C ALA* 4.0 14.1 - - + +
282C CYS* 3.9 38.1 - - - +
285C GLY* 3.5 18.1 - - - -
289C ASP 4.2 6.2 - - - +
292C VAL* 2.8 33.4 + - + +
294C GLU* 4.7 5.8 - - + -
312C VAL* 3.8 17.3 - - + +
313C ARG* 1.3 82.4 + - - +
315C GLY* 1.3 58.7 + - - +
318C GLY* 3.4 15.0 - - - +
319C ILE* 4.1 4.7 - - + -
320C GLU* 4.6 0.4 - - - -
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Residues in contact with GLY 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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282C CYS 4.7 0.9 - - - +
285C GLY* 2.9 22.5 - - - +
286C LEU* 3.5 4.5 + - - +
288C GLY* 5.9 0.4 - - - -
289C ASP 5.2 2.2 - - - -
313C ARG* 4.9 3.8 - - - -
314C LEU* 1.3 75.3 - - - +
316C ARG* 1.3 65.1 + - - -
317C ASN 3.2 4.8 + - - -
318C GLY* 2.7 21.2 + - - +
320C GLU* 3.6 18.2 - - - +
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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