Contacts of the strand formed by residues 335 - 339 (chain A) in PDB entry 1LC7
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 TYR 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLU* 2.5 26.6 + - - -
133A TRP* 3.2 34.7 + + - -
293A TYR* 3.4 12.5 + + - -
301A LEU* 4.0 17.7 - - + -
302A LEU 3.4 13.0 - - - -
303A ARG* 3.2 31.0 - - + -
324A SER* 4.1 0.5 + - - -
325A CYS* 2.9 38.7 + - + -
326A ALA 4.0 1.6 + - - -
330A GLY 5.6 0.2 - - - -
331A LEU* 4.2 15.7 - - + -
332A ASP* 3.1 43.5 + - - +
333A SER 4.5 0.7 - - - +
334A ARG* 1.3 81.4 - - - +
336A TYR* 1.3 72.2 + - - +
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Residues in contact with TYR 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 3.3 7.6 - - - +
302A LEU* 2.7 41.9 + - + +
304A CYS* 4.2 8.1 - - + -
309A ILE 3.6 8.3 + - - -
310A ASP* 3.6 9.8 + - - -
311A LEU* 3.2 42.9 + - + -
312A GLN* 3.6 22.9 - - + -
322A ILE* 3.6 27.1 - - + -
323A ARG 3.1 14.4 - - - +
324A SER* 3.9 14.8 - - - -
325A CYS* 3.8 5.8 - - - -
333A SER* 3.0 23.0 + - - -
334A ARG 3.3 19.7 - - - -
335A TYR* 1.3 78.3 - - - +
337A ARG* 1.3 63.6 + - - +
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Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE 3.7 2.4 - - - +
30A SER 2.8 25.7 + - - -
32A ASN* 3.4 23.4 + - - +
157A ASN* 3.0 20.4 + - - +
158A PRO* 3.8 20.4 - - + +
299A TYR* 3.8 28.3 - - + -
300A LEU 3.4 12.1 - - - +
301A LEU* 4.9 0.2 - - - -
322A ILE* 4.0 0.2 - - - +
323A ARG* 2.8 51.7 + - + +
325A CYS* 4.0 10.3 - - - -
328A TYR* 3.3 8.3 + - - -
336A TYR* 1.3 75.6 - - - +
338A VAL* 1.3 70.1 + - - +
990A TPO 2.8 46.5 + - - -
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.4 6.7 - - + -
32A ASN* 4.2 3.4 - - - -
280A PHE* 4.4 9.9 - - + -
284A LEU* 4.5 7.6 - - + -
299A TYR* 3.3 2.8 - - - +
300A LEU* 3.0 39.2 + - + +
302A LEU* 3.9 28.3 - - + -
322A ILE* 3.7 29.4 - - + -
337A ARG* 1.3 80.6 - - - +
339A ALA* 1.3 70.7 + - - +
349A LEU* 3.8 26.5 - - + -
353A LEU* 6.2 0.2 - - + -
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Residues in contact with ALA 339 (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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29A PHE* 2.9 34.2 + - - +
31A ALA 3.4 17.9 - - - +
32A ASN* 3.3 27.3 + - - +
33A ILE 5.2 1.6 - - - +
280A PHE* 3.4 11.1 - - - -
298A ASN* 3.7 2.9 - - - +
338A VAL* 1.3 79.1 - - - +
340A ILE* 1.3 63.3 + - - +
341A ARG* 4.0 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