Contacts of the strand formed by residues 293 - 299 (chain A) in PDB entry 4LEZ
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 ALA 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A LEU* 5.0 2.8 - - - +
267A ARG* 4.0 10.7 + - - -
287A GLU* 5.5 1.9 - - - +
288A LYS 6.0 0.2 + - - -
291A SER* 3.1 21.8 + - - +
292A PRO* 1.3 80.0 - - - +
294A VAL* 1.3 62.4 + - - +
295A THR* 3.8 7.6 + - - +
307A ASP* 3.9 33.2 - - + -
308A ILE 3.4 5.8 - - - +
309A ILE* 3.9 5.8 - - + +
602A 1SY 3.9 12.8 - - - +
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Residues in contact with VAL 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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263A LEU* 4.2 7.9 - - + -
266A PHE* 3.7 28.7 - - + -
267A ARG* 4.0 33.4 - - + +
270A ILE* 3.8 37.9 - - + -
284A VAL* 4.0 20.9 - - + -
293A ALA* 1.3 73.0 - - - +
295A THR* 1.3 61.1 + - - +
296A LEU* 4.6 1.5 - - + +
306A VAL 3.5 2.1 - - - +
308A ILE* 2.8 37.6 + - - +
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Residues in contact with THR 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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267A ARG* 5.0 2.6 - - - +
284A VAL* 3.6 5.6 - - - +
285A GLU* 2.8 67.8 + - - +
288A LYS* 5.6 3.6 + - - +
291A SER* 5.0 2.4 + - - -
293A ALA* 3.8 8.6 + - - +
294A VAL* 1.3 74.5 - - - +
296A LEU* 1.3 70.5 + - - +
297A LEU* 4.1 1.6 - - + -
305A SER* 4.1 14.6 - - - +
306A VAL 3.4 4.5 - - - +
307A ASP* 2.8 28.5 + - - +
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Residues in contact with LEU 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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174A VAL* 3.6 31.2 - - + -
178A LEU* 3.8 15.5 - - + -
270A ILE* 4.0 12.6 - - + -
274A VAL* 3.9 13.9 - - + -
282A VAL* 4.1 10.8 - - + -
283A SER 3.4 5.4 - - - +
284A VAL* 3.9 26.2 - - + -
294A VAL* 4.8 3.1 - - + +
295A THR* 1.3 77.4 - - - +
297A LEU* 1.3 65.0 + - - +
298A ILE* 4.0 1.6 - - + -
305A SER* 3.3 7.1 - - - -
306A VAL* 2.9 53.2 + - + +
308A ILE* 4.2 13.0 - - + -
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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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281A ASP* 3.7 1.0 - - - +
282A VAL* 3.4 1.9 - - - -
283A SER* 2.8 47.1 + - - +
284A VAL 4.9 0.9 - - - -
285A GLU* 3.6 51.4 - - + +
295A THR* 4.1 1.1 - - + -
296A LEU* 1.3 82.4 - - - +
298A ILE* 1.3 62.5 + - - +
299A ARG* 4.0 3.2 + - + +
303A GLU* 6.6 0.2 - - + -
304A ILE 3.5 4.7 - - - +
305A SER* 3.8 15.7 - - - +
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Residues in contact with ILE 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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170A THR* 3.9 19.1 - - + -
171A VAL* 4.5 15.0 - - + -
174A VAL* 4.2 23.6 - - + -
280A ILE* 5.1 2.5 - - + -
281A ASP 3.3 7.2 - - - +
282A VAL* 3.7 24.7 - - + -
296A LEU* 5.0 1.6 - - + -
297A LEU* 1.3 74.3 - - - +
299A ARG* 1.3 64.3 + - - +
300A ASN* 3.7 24.0 - - + +
302A GLU 3.3 3.8 - - - +
303A GLU* 3.4 3.6 - - - +
304A ILE* 2.9 42.6 + - + +
306A VAL* 3.8 27.4 - - + -
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Residues in contact with ARG 299 (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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280A ILE* 5.2 2.6 - - - +
281A ASP* 2.7 55.2 + - + +
283A SER* 6.1 0.4 - - - +
297A LEU* 5.3 3.4 - - + +
298A ILE* 1.3 72.4 - - - +
300A ASN* 1.3 59.7 + - - +
301A PRO* 3.2 25.2 + - + +
302A GLU 3.8 0.2 - - - -
303A GLU* 2.6 40.9 + - - +
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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