Contacts of the strand formed by residues 270 - 281 (chain A) in PDB entry 1LKF
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 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A TYR* 3.6 43.7 + - + -
249A MET* 2.9 56.8 + - + +
268A ASN* 3.3 4.7 + - - -
269A PHE* 1.3 86.1 - - + +
271A THR* 1.3 62.0 + - - +
272A ARG* 3.7 19.4 - - - +
297A ASN 3.3 5.8 - - - -
298A ASN* 3.4 26.5 - - - +
299A LYS* 5.9 1.8 - - - -
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Residues in contact with THR 271 (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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246A GLN* 3.6 31.0 - - + +
247A ARG 3.5 13.9 - - - +
248A GLU* 5.0 0.4 - - + -
249A MET* 5.3 0.4 - - - -
268A ASN* 2.6 32.7 + - - +
270A LYS* 1.3 71.2 - - - +
272A ARG* 1.3 76.4 + - - +
273A THR* 3.8 5.4 - - - +
295A THR 4.6 0.2 - - - -
296A GLU* 3.3 1.8 - - - -
297A ASN* 2.8 53.0 + - - +
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Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 3.6 27.0 - - + -
32A ILE* 4.1 4.0 - - - +
246A GLN* 3.4 2.9 - - - -
247A ARG* 3.2 66.9 + - - +
249A MET* 4.1 9.2 - - - +
270A LYS* 3.7 20.3 - - - +
271A THR* 1.3 103.1 + - - +
273A THR* 1.3 62.4 + - - +
295A THR 3.7 1.3 - - - -
296A GLU* 3.6 33.6 + - - +
297A ASN 3.0 19.4 + - - +
298A ASN* 2.9 23.2 + - - +
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Residues in contact with THR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 3.2 9.9 - - - -
32A ILE* 4.7 0.2 - - - -
244A THR* 3.3 30.5 - - + -
245A TYR 3.7 3.6 - - - +
246A GLN* 3.0 28.4 + - + +
271A THR* 3.8 5.9 - - - +
272A ARG* 1.3 75.8 - - - +
274A PHE* 1.3 66.8 + - - +
275A LYS* 4.2 3.8 - - + +
293A LYS 3.6 0.4 - - - +
294A GLU* 3.4 1.7 - - - -
295A THR* 2.8 53.4 + - - +
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Residues in contact with PHE 274 (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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1A GLU 4.3 0.7 - - - -
25A ALA* 3.3 37.7 - - + -
26A ASP 3.5 29.4 - - - -
27A SER* 3.7 18.8 - - - -
30A PHE* 4.8 0.4 - - + -
32A ILE* 4.1 24.7 - - + +
34A GLN* 3.5 27.1 - - + +
244A THR* 3.3 2.3 - - - -
245A TYR 2.9 37.6 + - - +
273A THR* 1.3 76.6 - - - +
275A LYS* 1.3 64.3 + - - +
276A SER* 4.9 1.8 - - - -
292A THR* 4.1 26.7 - - + -
293A LYS 3.6 3.6 - - - -
294A GLU* 3.9 18.4 - - + -
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLN* 4.1 9.7 + - - -
242A THR* 3.4 33.5 + - - +
243A VAL 3.3 4.9 - - - +
244A THR* 3.6 22.2 - - + +
273A THR* 4.2 2.9 - - + -
274A PHE* 1.3 77.9 - - - +
276A SER* 1.3 66.5 + - - +
277A THR* 3.6 10.0 + - - +
291A ASP* 5.6 3.4 - - - -
292A THR* 3.3 5.7 - - - +
293A LYS* 2.9 50.7 + - + +
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Residues in contact with SER 276 (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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25A ALA* 4.1 13.0 - - - -
34A GLN* 2.6 31.2 + - - +
242A THR* 3.1 7.4 - - - -
243A VAL* 2.8 36.5 + - - +
274A PHE* 4.9 0.7 - - - -
275A LYS* 1.3 75.7 - - - +
277A THR* 1.3 62.8 + - - +
278A TYR* 3.2 27.5 - - - -
289A LEU* 4.4 1.6 - - - -
291A ASP 3.4 7.6 - - - -
292A THR* 4.4 1.8 - - - +
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Residues in contact with THR 277 (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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240A LYS* 4.2 30.1 - - + +
241A ILE 3.3 10.5 - - - +
242A THR* 3.4 21.7 - - + +
275A LYS* 3.6 11.6 + - - +
276A SER* 1.3 73.3 - - - +
278A TYR* 1.3 63.6 + - - +
289A LEU* 3.5 5.5 - - - +
290A LEU* 2.8 33.7 + - + -
291A ASP* 2.8 32.1 + - + +
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Residues in contact with TYR 278 (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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4A ILE* 4.2 6.1 - - + +
23A ALA* 3.5 31.2 - - + +
24A THR 4.1 6.8 + - - -
25A ALA* 3.6 20.4 + - - +
34A GLN* 4.8 0.2 - - - -
36A LEU* 3.6 19.4 - - + +
38A PHE* 4.6 6.3 - + + -
240A LYS* 3.5 5.7 - - - +
241A ILE* 2.8 49.1 + - + +
243A VAL* 5.4 1.6 - - + -
276A SER* 3.2 31.2 - - - -
277A THR* 1.3 77.0 - - - +
279A GLU* 1.3 65.0 + - - +
280A ILE* 3.8 1.1 + - + -
287A VAL* 4.3 13.2 - - + -
288A LYS 3.3 11.2 - - - -
289A LEU* 3.6 40.5 - - + +
290A LEU* 4.2 4.0 - - - -
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Residues in contact with GLU 279 (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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238A LYS* 3.3 47.7 + - + +
239A SER 3.5 9.6 - - - +
240A LYS* 4.6 2.0 - - + +
278A TYR* 1.3 72.2 - - - +
280A ILE* 1.3 63.1 + - - +
281A ASP* 3.8 3.0 + - - +
287A VAL* 3.3 5.2 - - - -
288A LYS* 2.8 54.2 + - + +
290A LEU* 3.8 27.3 - - + +
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Residues in contact with ILE 280 (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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38A PHE* 4.3 11.7 - - + -
40A PHE* 3.5 34.3 - - + -
51A LEU* 3.6 22.4 - - + -
229A LEU* 4.6 4.7 - - + -
238A LYS* 2.9 28.6 - - - +
239A SER* 2.7 32.4 + - - +
240A LYS 5.3 0.2 - - - +
241A ILE* 3.7 42.8 - - + -
278A TYR 5.0 0.2 - - - -
279A GLU* 1.3 73.9 - - - +
281A ASP* 1.3 61.2 + - - +
282A TRP* 3.6 18.1 + - + +
286A LYS 3.9 2.9 - - - -
287A VAL* 4.3 3.6 - - + -
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Residues in contact with ASP 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 4.2 0.5 - - - -
237A LYS* 3.9 5.3 - - - +
238A LYS* 3.7 30.3 + - + +
279A GLU* 3.8 3.7 + - - +
280A ILE* 1.3 72.3 - - - +
282A TRP* 1.3 52.7 + - - +
283A GLU* 3.2 10.2 + - - +
284A ASN* 3.0 44.8 + - - +
285A HIS* 2.8 32.6 + - - -
286A LYS* 2.8 32.1 + - + +
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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