Contacts of the strand formed by residues 307 - 315 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168H VAL* 3.6 26.7 - - + -
169H PRO* 4.1 24.7 - - + -
172H ALA* 3.5 27.8 - - + -
173H GLU* 5.6 2.9 - - - -
176H LYS* 5.6 5.4 - - - -
181H TYR* 3.7 17.7 - - - -
186H LEU* 4.4 5.4 - - + -
297H PHE* 3.7 24.9 - - + -
298H VAL 3.1 6.3 - - - +
299H SER* 3.6 22.0 - - - -
300H SER* 4.2 0.7 - - - +
305H LEU* 3.2 8.9 - - - +
306H PRO* 1.3 102.5 - - + +
308H PHE* 1.3 67.4 + - - +
343H LEU* 4.0 0.9 - - - +
347H ILE* 3.6 22.2 - - + +
351H VAL* 4.8 4.9 - - + -
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Residues in contact with PHE 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217H VAL* 3.9 1.1 - - + -
218H GLY* 3.4 24.9 - - - -
296H ALA 3.5 1.2 - - - +
297H PHE* 3.5 13.4 - - - -
298H VAL* 2.8 33.4 + - - +
300H SER* 3.3 20.4 + - - +
302H VAL* 4.7 6.3 - - + -
303H THR* 4.0 29.8 - - + +
305H LEU* 4.4 2.0 - - + +
307H PHE* 1.3 74.5 - - - +
309H ALA* 1.3 88.8 + - - +
310H SER* 4.8 1.7 + - - -
325H LEU* 3.4 24.5 - - + -
336H LEU* 3.4 33.4 - - + -
339H ALA* 5.4 1.8 - - + -
340H LYS* 4.7 7.0 - - + -
343H LEU* 3.6 21.8 - - + -
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Residues in contact with ALA 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190H THR* 4.6 10.8 - - + +
216H VAL 4.3 4.9 - - - +
217H VAL* 2.9 30.2 - - - +
218H GLY 2.8 29.8 + - - +
219H GLY 4.5 2.0 - - - +
296H ALA 3.0 17.5 - - - +
297H PHE* 3.9 9.6 - - + +
308H PHE* 1.3 83.5 - - - +
310H SER* 1.3 61.5 + - - +
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Residues in contact with SER 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216H VAL 4.8 0.4 + - - -
217H VAL* 3.6 17.7 - - - +
295H CYS* 3.1 6.7 - - - -
296H ALA 3.0 25.5 + - - +
298H VAL* 5.5 0.2 - - - +
300H SER* 5.3 0.3 - - - -
302H VAL* 4.3 3.3 - - - +
308H PHE* 4.1 5.1 + - - -
309H ALA* 1.3 76.9 - - - +
311H LYS* 1.3 73.3 + - - +
312H VAL* 3.4 6.4 + - - +
322H VAL* 3.6 14.4 - - - +
323H TYR 3.3 21.1 + - - -
324H SER 5.3 1.6 - - - -
325H LEU* 4.3 10.5 - - - -
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Residues in contact with LYS 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H PRO* 3.8 19.8 - - + +
217H VAL* 4.8 3.6 - - + +
228H LEU* 6.1 0.2 - - - -
231H GLN* 3.3 27.4 + - - +
293H ILE* 3.8 15.3 - - + -
294H GLU 3.7 5.8 - - - -
295H CYS* 4.1 16.8 - - - +
310H SER* 1.3 81.5 + - - +
312H VAL* 1.3 58.4 + - - +
323H TYR* 3.1 48.6 + - + +
324H SER 5.6 4.9 - - - +
325H LEU 5.4 2.7 - - - -
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Residues in contact with VAL 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H LEU* 4.5 4.7 - - + -
293H ILE* 3.5 1.6 - - - +
294H GLU* 2.9 35.8 + - + +
296H ALA* 4.3 16.6 - - + +
298H VAL* 4.0 27.1 - - + -
310H SER* 3.6 14.6 - - - +
311H LYS* 1.3 81.6 - - - +
313H ARG* 1.3 60.6 + - - +
314H LEU* 3.8 24.8 + - + +
319H ILE* 4.6 7.9 - - + -
321H GLU 3.4 12.8 - - - +
322H VAL* 4.4 7.0 - - + -
323H TYR* 3.9 4.0 - - - -
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Residues in contact with ARG 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291H GLY* 4.6 13.5 - - - +
292H VAL 3.2 19.7 - - - +
293H ILE* 4.1 9.0 - - + -
312H VAL* 1.3 73.7 - - - +
314H LEU* 1.3 65.8 + - - +
318H GLY 3.5 0.5 - - - +
319H ILE* 3.7 5.0 - - - -
320H GLU* 3.0 44.2 + - + +
321H GLU* 2.8 54.2 + - - +
323H TYR* 2.8 27.7 + - + +
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Residues in contact with LEU 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H ILE* 6.4 0.2 - - + -
187H LEU* 3.7 26.9 - - + -
278H PHE* 4.3 12.3 - - + -
281H ALA* 3.9 20.2 - - + +
282H CYS* 3.7 39.0 - - - +
285H GLY* 3.4 13.9 - - - -
289H ASP 4.3 4.3 - - - +
292H VAL* 2.8 33.4 + - + +
294H GLU* 4.9 4.7 - - + +
312H VAL* 4.0 15.7 - - + +
313H ARG* 1.3 83.0 - - - +
315H GLY* 1.3 59.5 + - - +
318H GLY* 3.4 15.7 - - - +
319H ILE* 4.4 1.6 - - - +
320H GLU* 4.0 1.8 - - - -
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Residues in contact with GLY 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282H CYS 4.5 0.9 - - - +
285H GLY* 3.0 24.0 - - - -
286H LEU* 3.3 5.5 + - - +
289H ASP 5.1 3.4 - - - -
314H LEU* 1.3 75.0 - - - +
316H ARG* 1.3 65.6 + - - -
317H ASN 3.2 2.9 - - - -
318H GLY* 2.7 22.2 + - - -
320H GLU* 3.3 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