Contacts of the strand formed by residues 284 - 292 (chain A) in PDB entry 8LDH
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 VAL 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A TYR* 5.2 0.9 - - - -
273A MET* 4.0 3.2 - - - +
274A VAL* 3.2 28.1 + - + +
275A LYS 4.3 1.4 + - - -
280A ILE* 4.6 2.2 - - + -
282A ASP* 3.1 28.0 + - - +
283A ASN* 1.3 77.9 - - - +
285A PHE* 1.3 66.5 + - - +
286A LEU* 4.4 3.6 - - + -
317A ALA* 3.3 50.7 - - + +
320A LEU* 3.6 29.4 - - + -
321A TRP* 4.2 6.7 - - + -
324A GLN* 4.6 4.7 - - - +
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Residues in contact with PHE 285 (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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141A ASP* 3.3 31.7 + - - +
144A THR* 3.3 25.8 - - + -
145A TYR* 3.8 25.4 - + + +
148A TRP* 3.8 44.6 - + + -
155A MET* 4.5 7.9 - - + -
158A ILE* 3.7 19.3 - - + -
271A SER* 3.2 14.4 - - - +
272A THR* 2.8 26.5 - - - -
273A MET* 3.6 29.2 - - + -
284A VAL* 1.3 73.1 - - - +
286A LEU* 1.3 67.4 + - - +
320A LEU* 4.0 4.3 - - - +
324A GLN* 5.8 0.2 + - - -
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Residues in contact with LEU 286 (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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141A ASP* 3.9 6.1 - - - +
191A GLY* 4.0 6.7 - - - +
192A GLU* 3.5 35.4 - - + +
271A SER* 3.4 6.5 + - - -
272A THR* 2.8 31.2 + - - +
274A VAL* 3.3 21.0 - - + +
280A ILE* 3.7 30.3 - - + -
284A VAL* 4.4 3.4 - - + -
285A PHE* 1.3 73.5 - - - +
287A SER* 1.3 60.7 + - - +
288A LEU* 5.7 1.3 - - + -
313A LEU* 3.7 22.4 - - + +
316A SER* 3.6 9.0 - - - -
317A ALA* 4.5 5.4 - - + -
320A LEU* 3.5 22.2 - - + -
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Residues in contact with SER 287 (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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141A ASP* 4.5 0.9 + - - -
162A GLY* 3.6 4.2 - - - -
163A CYS* 2.9 42.7 + - - +
190A ILE* 3.3 6.7 - - - +
191A GLY* 3.1 35.7 + - - -
269A PRO* 3.7 4.6 + - - -
270A VAL 3.2 18.3 - - - -
271A SER* 3.6 0.3 + - - -
286A LEU* 1.3 73.0 - - - +
288A LEU* 1.3 79.1 + - - +
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Residues in contact with LEU 288 (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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190A ILE* 4.4 12.6 - - + -
268A HIS 3.1 13.0 - - - +
269A PRO* 3.9 5.4 - - - -
270A VAL 3.3 14.9 + - - +
272A THR* 4.1 7.9 - - - +
274A VAL* 4.2 20.2 - - + -
277A PHE* 4.4 6.5 - - + -
278A TYR* 3.8 36.1 - - + +
286A LEU* 3.8 2.2 + - + +
287A SER* 1.3 94.5 - - - +
289A PRO* 1.3 74.6 - - + +
290A CYS* 3.3 4.2 + - - -
300A ILE* 3.0 39.5 - - + -
301A VAL 5.0 0.4 - - - +
303A MET* 5.1 2.2 - - + -
313A LEU* 4.9 9.2 - - + -
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Residues in contact with PRO 289 (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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188A TRP* 4.0 20.0 - - + -
190A ILE* 4.8 2.7 - - + -
267A VAL* 3.8 14.1 - - + -
268A HIS 3.4 9.6 - - - +
269A PRO* 4.2 2.2 - - + -
288A LEU* 1.3 89.3 - - + +
290A CYS* 1.3 56.7 + - - +
300A ILE* 3.7 1.9 - - - +
301A VAL* 2.6 61.3 + - + +
303A MET* 3.7 36.1 - - + -
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Residues in contact with CYS 290 (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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266A ARG 3.2 1.6 - - - +
267A VAL* 3.1 4.5 - - - -
268A HIS* 2.6 44.8 + - - +
270A VAL* 4.2 3.8 - - + -
272A THR* 3.2 30.7 - - - -
288A LEU 3.3 15.3 - - - -
289A PRO* 1.3 76.2 - - - +
291A VAL* 1.3 58.9 + - - +
292A LEU* 3.9 2.6 + - + +
297A ILE* 3.6 31.6 - - + -
299A ASN 3.2 17.0 - - - +
300A ILE* 4.3 8.7 - - - -
301A VAL* 4.8 0.2 - - - -
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Residues in contact with VAL 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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265A CYS* 3.6 32.8 - - + +
266A ARG 3.2 5.8 - - - -
267A VAL* 3.7 21.8 - - + -
289A PRO 4.4 0.4 + - - -
290A CYS* 1.3 74.6 - - - +
292A LEU* 1.3 65.7 + - - +
297A ILE 4.0 0.2 - - - -
298A SER* 3.1 42.4 + - - +
299A ASN* 3.1 29.3 + - + +
301A VAL* 4.6 8.7 - - + -
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Residues in contact with LEU 292 (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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159A ILE* 3.8 11.2 - - + -
256A LEU* 4.2 19.1 - - + +
259A THR* 3.2 17.2 - - + +
260A ILE* 3.9 28.0 - - + -
265A CYS* 2.5 38.1 + - - -
266A ARG 3.0 12.2 + - - +
268A HIS* 4.2 17.9 - - + -
270A VAL* 4.2 8.5 - - + -
290A CYS* 4.2 9.9 - - + +
291A VAL* 1.3 82.7 - - - +
293A ASN* 1.3 56.2 + - - +
296A GLY 3.5 5.2 - - - +
297A ILE* 3.1 37.9 - - + -
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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