Contacts of the helix formed by residues 290 - 302 (chain A) in PDB entry 4L7F
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 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A HIS* 3.9 5.4 - - - -
284A SER 5.6 2.0 - - - +
285A GLU 3.2 26.5 + - - +
286A HIS* 3.6 10.1 + - - +
287A ASN 2.9 23.8 + - - -
288A LYS 4.5 4.3 - - - +
289A LEU* 1.3 78.0 - - - +
291A ALA* 1.3 63.8 + - - +
292A SER* 3.5 20.9 - - - +
293A GLN* 2.8 42.1 + - - +
294A ALA 3.1 9.9 + - - -
320A TYR* 3.8 5.7 - - - -
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Residues in contact with ALA 291 (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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125A HIS* 3.7 16.4 + - + +
277A ASP* 3.6 23.1 - - - +
280A PHE* 3.6 37.9 - - + -
284A SER 5.9 0.2 + - - -
290A LYS* 1.3 72.0 - - - +
292A SER* 1.3 57.5 + - - +
294A ALA* 3.3 2.1 + - - +
295A ARG* 2.8 33.6 + - - +
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Residues in contact with SER 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ASP* 5.2 0.2 + - - -
290A LYS* 3.5 15.5 - - - +
291A ALA* 1.3 79.7 - - - +
293A GLN* 1.3 61.4 + - - +
295A ARG* 3.7 20.6 - - - +
296A ASP* 2.9 28.6 + - - +
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Residues in contact with GLN 293 (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 LYS 4.3 7.3 + - - -
289A LEU* 3.3 18.6 - - - +
290A LYS* 2.8 45.9 + - + +
292A SER* 1.3 77.3 + - - +
294A ALA* 1.3 64.8 + - - +
296A ASP* 3.3 3.0 + - - -
297A LEU* 3.0 19.8 + - - +
318A HIS* 3.1 15.8 - - + -
319A PRO* 4.2 23.6 + - + +
320A TYR* 4.0 16.6 - - + +
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Residues in contact with ALA 294 (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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215A MET* 3.5 29.6 - - + +
219A VAL* 5.6 0.2 - - + -
280A PHE* 3.6 29.2 - - + -
290A LYS 3.1 5.7 + - - +
291A ALA 3.3 2.7 + - - +
293A GLN* 1.3 79.0 - - - +
295A ARG* 1.3 57.8 + - - +
297A LEU* 3.3 1.1 + - - -
298A LEU* 2.9 29.6 + - + +
320A TYR* 3.7 25.4 - - + -
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Residues in contact with ARG 295 (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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271A PHE* 3.6 30.6 + - + +
272A GLU* 3.6 38.4 - - - +
275A PHE* 2.8 31.6 + - + +
276A PRO* 3.6 1.8 - - - +
277A ASP* 2.8 37.8 + - - +
280A PHE* 4.0 10.8 - - + -
291A ALA* 2.8 20.3 + - - +
292A SER* 3.7 31.0 - - - +
294A ALA* 1.3 73.4 - - - +
296A ASP* 1.3 56.5 + - - +
298A LEU* 3.3 12.1 + - - +
299A SER* 3.0 28.6 + - - -
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Residues in contact with ASP 296 (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 SER 2.9 19.5 + - - +
293A GLN* 3.5 7.4 - - - +
295A ARG* 1.3 72.5 - - - +
297A LEU* 1.3 66.5 + - - +
299A SER* 2.7 24.8 + - - -
300A LYS* 2.8 39.8 + - - +
318A HIS* 2.6 25.3 + - + +
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Residues in contact with LEU 297 (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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132A LEU* 5.8 0.4 - - + -
136A LEU* 5.5 1.1 - - + -
215A MET* 4.0 20.2 - - + -
293A GLN 3.0 8.2 + - - +
294A ALA* 3.7 6.7 - - - +
296A ASP* 1.3 76.8 - - - +
298A LEU* 1.3 65.3 + - - +
300A LYS* 3.0 11.6 + - - -
301A MET* 3.1 42.2 + - + +
310A ILE* 4.2 15.0 - - + -
315A ALA* 4.4 6.7 - - + -
318A HIS* 3.6 37.4 + - + +
320A TYR* 4.3 5.4 - - + -
321A ILE* 3.6 36.1 - - + -
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Residues in contact with LEU 298 (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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212A GLY* 3.5 27.1 - - - +
215A MET* 3.8 24.9 - - + -
216A GLY* 3.6 13.9 - - - +
219A VAL* 4.5 12.1 - - + -
271A PHE* 3.7 12.1 - - + -
275A PHE* 3.9 30.5 - - + -
280A PHE* 4.8 2.2 - - + -
294A ALA 2.9 23.7 + - - +
295A ARG* 3.5 8.1 - - - +
297A LEU* 1.3 76.7 - - - +
299A SER* 1.3 55.4 + - - +
301A MET* 4.6 4.5 - - - +
302A LEU* 2.9 52.2 + - + +
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Residues in contact with SER 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 3.7 38.2 - - - -
295A ARG 3.0 13.8 + - - -
296A ASP* 2.7 26.5 + - - -
298A LEU* 1.3 74.9 - - - +
300A LYS* 1.3 62.9 + - - +
303A VAL* 3.1 19.0 - - - +
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Residues in contact with LYS 300 (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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296A ASP* 2.8 43.0 + - - +
297A LEU* 3.0 7.6 + - - +
299A SER* 1.3 81.5 - - - +
301A MET* 1.3 61.1 + - - +
303A VAL* 3.5 9.8 - - - +
308A LYS 5.8 0.4 - - - -
309A ARG* 3.4 6.1 - - - +
310A ILE* 3.1 55.9 + - + +
318A HIS* 4.3 10.7 + - + -
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Residues in contact with MET 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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132A LEU* 5.6 0.2 - - + -
136A LEU* 5.1 1.6 - - - -
208A LEU* 3.0 56.5 - - + +
209A TRP* 3.9 8.7 - - - -
211A VAL* 4.0 15.0 - - + -
212A GLY* 3.6 24.5 - - - +
215A MET* 3.6 29.2 - - - -
297A LEU* 3.1 34.1 + - + +
298A LEU* 4.2 2.7 - - - +
300A LYS* 1.3 77.9 - - - +
302A LEU* 1.3 57.9 + - - +
303A VAL 2.9 11.7 + - - -
309A ARG* 3.3 20.7 + - - -
310A ILE* 3.7 4.7 - - + -
315A ALA* 4.8 2.0 - - - -
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Residues in contact with LEU 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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209A TRP* 3.7 20.9 - - + +
212A GLY* 3.8 24.7 - - - +
213A CYS* 3.8 21.1 - - - +
224A LEU* 3.6 24.5 - - + -
225A PHE* 4.1 15.3 - - + -
241A LEU* 3.7 18.1 - - + +
271A PHE* 3.7 31.6 - - + -
275A PHE* 4.4 4.7 - - + -
298A LEU* 2.9 35.9 + - + +
301A MET* 1.3 71.8 - - - +
303A VAL* 1.3 61.4 + - - +
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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