Contacts of the strand formed by residues 300 - 309 (chain A) in PDB entry 5C7Z
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 LYS 300 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A GLU* 3.9 1.4 - - - +
296A VAL* 3.0 61.6 + - + +
297A GLY 5.2 0.5 - - - +
298A ARG 3.8 0.8 - - - -
299A THR* 1.3 93.4 + - - +
301A LEU* 1.3 67.2 + - - +
302A GLU* 5.4 0.9 - - + +
369A GLU* 3.6 37.9 + - + +
370A ILE 3.0 17.7 - - - +
371A GLU* 4.3 8.7 - - + -
372A LEU* 4.1 7.2 - - - +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A VAL* 4.2 14.8 - - + -
294A ARG 3.4 6.3 - - - +
295A GLU* 3.7 31.6 - - + +
300A LYS* 1.3 79.9 - - - +
302A GLU* 1.3 62.5 + - - +
303A VAL* 3.9 6.2 + - + -
327A PRO* 4.2 22.2 - - + -
368A ALA 3.8 0.9 - - - +
369A GLU* 3.4 3.9 - - - -
370A ILE* 2.7 66.2 + - + +
372A LEU* 4.1 14.6 - - + -
381A TRP* 4.2 19.5 - - + -
383A ARG* 5.9 0.7 - - - +
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LEU 3.7 0.5 - - - +
293A VAL* 3.4 3.3 - - - +
294A ARG* 2.7 73.4 + - + +
296A VAL* 4.0 13.2 - - + -
300A LYS* 4.3 1.4 - - + +
301A LEU* 1.3 73.7 - - - +
303A VAL* 1.3 64.8 + - - +
367A SER* 5.6 3.6 - - - -
368A ALA 3.8 10.7 + - - +
369A GLU* 3.1 33.4 - - + +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A PRO* 6.3 0.2 - - + -
292A LEU 3.3 6.7 - - - +
293A VAL* 4.4 18.8 - - + -
301A LEU* 4.3 9.4 - - + +
302A GLU* 1.3 83.7 + - - +
304A LYS* 1.3 64.0 + - - +
305A VAL* 4.0 21.3 - - + -
324A ILE* 4.4 21.1 - - + -
351A ILE* 6.1 0.2 - - + -
366A ILE* 3.9 0.6 - - + +
367A SER* 3.3 3.5 - - - -
368A ALA* 2.7 50.3 + - + +
370A ILE* 4.0 25.8 - - + -
386A ILE* 6.0 0.7 - - + -
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Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ILE 3.8 1.0 - - - +
291A PRO* 3.6 0.7 - - - +
292A LEU* 2.9 58.8 + - + +
303A VAL* 1.3 72.9 - - - +
305A VAL* 1.3 66.7 + - - +
306A VAL* 3.7 22.4 - - - +
365A GLN* 3.5 35.8 - - - +
366A ILE 3.4 6.3 - - - +
367A SER* 3.6 21.5 - - - +
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A VAL* 3.9 27.1 - - + -
290A ILE 3.5 3.8 - - - +
291A PRO* 4.3 4.0 - - + -
303A VAL* 4.0 12.1 - - + -
304A LYS* 1.3 82.2 - - - +
306A VAL* 1.3 68.3 + - - +
307A ILE* 4.5 7.4 - - + -
322A VAL* 4.6 11.0 - - + -
324A ILE* 3.9 15.9 - - + -
353A TRP* 4.2 1.7 - - + -
365A GLN* 3.2 2.4 - - - +
366A ILE* 2.8 49.1 + - + +
386A ILE* 3.8 24.0 - - + -
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A ARG 3.7 0.9 - - - +
289A VAL* 3.5 3.3 - - - -
290A ILE* 2.8 58.0 + - + +
304A LYS* 3.7 32.1 - - - +
305A VAL* 1.3 74.5 - - - +
307A ILE* 1.3 73.6 + - - +
308A LYS* 4.4 3.6 - - + -
363A GLU* 4.0 26.5 - - + +
364A SER 3.2 9.4 - - - +
365A GLN* 3.7 13.9 - - + +
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A PHE* 4.5 7.9 - - + -
288A ARG 3.3 7.9 - - - +
289A VAL* 4.4 8.1 - - + -
305A VAL* 4.5 7.2 - - + -
306A VAL* 1.3 79.9 - - - +
308A LYS* 1.3 62.5 + - - +
309A SER 4.3 0.2 - - - -
320A ILE* 4.3 4.9 - - + -
322A VAL* 4.1 20.9 - - + -
353A TRP* 4.1 14.3 - - + -
355A ILE* 3.9 27.6 - - + -
358A MET* 4.0 18.8 - - + +
363A GLU* 3.3 4.9 - - - -
364A SER* 2.8 42.5 + - - +
388A MET* 4.3 25.6 - - + -
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Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A PHE* 3.4 9.0 - - - -
288A ARG* 2.9 44.3 + - + +
290A ILE* 3.7 26.7 - - + -
306A VAL* 4.4 5.4 - - + -
307A ILE* 1.3 73.2 - - - +
309A SER* 1.3 64.5 + - - +
310A ASN* 3.5 2.5 + - + +
362A LYS 3.2 5.8 - - - +
363A GLU* 2.6 49.4 + - + +
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A PRO 3.7 5.4 - - - -
287A PHE* 4.0 12.1 - - - -
308A LYS* 1.3 72.5 - - - +
310A ASN* 1.3 59.6 + - - +
311A PHE* 3.6 20.9 - - - -
358A MET* 3.4 14.4 - - - +
359A ALA 2.5 30.2 + - - -
361A MET* 2.8 30.1 + - - +
362A LYS 3.0 18.0 + - - +
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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