Contacts of the strand formed by residues 238 - 255 (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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A SER* 5.1 0.2 + - - -
91A ASN* 2.8 20.6 + - - +
236A ALA* 3.8 7.3 - - + +
237A LYS* 1.3 84.4 - - + +
239A SER* 1.3 61.6 + - - +
279A GLU* 3.3 39.5 + - + +
280A ILE 2.9 12.6 - - - +
281A ASP* 3.7 28.4 + - + +
282A TRP* 4.4 0.9 - - - -
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Residues in contact with SER 239 (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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88A SER* 5.0 0.7 + - - -
90A SER* 3.8 10.5 - - - -
91A ASN* 3.6 19.5 - - - -
94A VAL* 3.7 20.1 - - - +
229A LEU* 5.6 0.2 - - - +
238A LYS* 1.3 76.2 - - - +
240A LYS* 1.3 62.0 + - - +
279A GLU* 3.5 4.8 - - - -
280A ILE* 2.7 43.4 + - - +
282A TRP* 2.9 22.6 + - - -
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Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER* 3.6 8.0 + - - -
89A GLN* 2.8 41.8 + - + +
90A SER* 3.1 25.2 + - - +
239A SER* 1.3 77.5 + - - +
241A ILE* 1.3 61.4 + - - +
277A THR* 4.2 14.2 - - + +
278A TYR 3.5 4.7 - - - +
279A GLU* 5.0 2.2 - - + -
280A ILE* 5.3 0.2 - - - +
290A LEU* 3.6 34.1 - - + -
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 4.5 9.2 - - + -
51A LEU* 5.2 0.7 - - + -
53A LEU* 3.8 17.7 - - + -
86A ILE* 3.8 26.0 - - + -
87A SER 3.2 17.0 - - - +
89A GLN 4.4 0.2 - - - +
229A LEU* 3.7 28.5 - - + -
240A LYS* 1.3 75.1 - - - +
242A THR* 1.3 65.5 + - - +
243A VAL* 4.9 4.9 - - + -
276A SER 4.0 0.2 - - - +
277A THR* 3.3 4.3 - - - +
278A TYR* 2.8 56.7 + - + +
280A ILE* 3.7 24.7 - - + -
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Residues in contact with THR 242 (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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85A SER 3.7 0.9 - - - +
86A ILE* 3.4 5.0 - - - +
87A SER* 2.9 49.0 + - - -
89A GLN* 3.5 29.4 + - + +
241A ILE* 1.3 77.0 - - - +
243A VAL* 1.3 63.8 + - - +
244A THR* 4.9 3.4 + - - -
275A LYS* 3.4 23.8 - - - +
276A SER 3.1 7.4 - - - -
277A THR* 3.4 26.9 - - + +
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 3.0 19.4 - - - +
36A LEU* 3.8 31.6 - - + -
38A PHE* 5.7 0.4 - - + -
53A LEU* 4.3 11.0 - - + -
55A ALA* 4.9 0.2 - - + -
84A VAL* 5.0 0.4 - - + -
85A SER 3.3 7.6 - - - +
86A ILE* 4.0 24.2 - - + -
241A ILE* 4.9 9.4 - - + -
242A THR* 1.3 80.0 - - - +
244A THR* 1.3 61.4 + - - +
245A TYR* 3.7 20.9 - - + -
275A LYS* 3.3 0.7 - - - -
276A SER* 2.8 41.1 + - - +
278A TYR* 5.4 0.9 - - + -
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Residues in contact with THR 244 (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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83A ASN 3.5 0.8 - - - +
84A VAL* 3.1 6.2 - - - -
85A SER* 2.8 52.9 + - - +
242A THR* 4.9 4.0 + - - -
243A VAL* 1.3 74.9 + - - +
245A TYR* 1.3 68.3 + - - +
246A GLN* 4.1 6.1 - - + +
273A THR* 3.3 34.1 - - + -
274A PHE 3.3 5.8 - - - +
275A LYS* 3.6 20.6 - - + +
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Residues in contact with TYR 245 (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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32A ILE* 3.5 25.7 - - + +
33A SER 3.4 18.8 - - - -
34A GLN* 3.5 23.8 - - + +
35A ILE 4.2 0.2 + - - -
36A LEU* 4.0 4.9 - - - +
55A ALA* 3.3 11.7 - - + +
56A THR 2.6 41.7 + - - -
59A ILE* 3.7 24.2 - - + -
83A ASN 3.4 3.4 - - - -
84A VAL* 3.6 24.2 - - + -
223A PRO* 3.8 15.7 - - + -
243A VAL* 3.7 16.8 - - + -
244A THR* 1.3 81.3 - - - +
246A GLN* 1.3 61.9 + - - +
273A THR* 3.7 0.7 - - - +
274A PHE* 2.9 31.1 + - - +
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Residues in contact with GLN 246 (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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32A ILE* 4.9 1.6 - - - -
59A ILE* 4.0 9.4 - - - +
82A TYR* 3.3 7.1 - - - +
83A ASN* 2.7 66.2 + - + +
244A THR* 4.7 5.8 - - + +
245A TYR* 1.3 76.0 - - - +
247A ARG* 1.3 72.0 + - - +
248A GLU* 4.1 5.6 - - - +
271A THR* 3.6 15.2 - - + +
272A ARG 3.4 8.1 - - - +
273A THR* 3.0 35.4 + - + +
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Residues in contact with ARG 247 (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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30A PHE* 2.8 37.0 + - - +
31A LYS* 5.4 0.4 - - - +
32A ILE* 3.9 15.4 - - - +
59A ILE* 4.1 6.3 - - + -
60A ASN* 3.1 36.3 + - - +
61A SER 3.3 15.9 - - - +
62A GLY* 3.6 15.6 - - - -
79A GLY* 5.7 0.9 - - - -
81A LYS 3.3 6.7 - - - +
82A TYR* 4.2 6.7 - - + -
246A GLN* 1.3 76.4 - - - +
248A GLU* 1.3 64.9 + - - +
249A MET* 3.4 23.4 + - + +
271A THR* 3.5 10.4 - - - +
272A ARG* 3.2 48.5 + - + +
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Residues in contact with GLU 248 (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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79A GLY* 3.9 2.9 - - - -
80A ALA* 3.0 24.4 + - - -
81A LYS* 2.8 29.1 + - + +
83A ASN* 3.0 30.9 + - - +
181A ARG* 3.1 34.0 + - - +
246A GLN* 4.1 7.5 - - - +
247A ARG* 1.3 74.8 - - - +
249A MET* 1.3 60.8 + - - +
250A ASP* 4.6 1.1 - - - -
267A LYS* 5.4 1.2 - - - +
268A ASN* 3.3 35.1 - - - +
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Residues in contact with MET 249 (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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61A SER 3.7 18.8 - - - +
62A GLY* 3.4 23.3 - - - +
64A VAL* 5.2 3.4 - - + -
77A TYR* 4.4 16.5 - - + -
78A TRP 3.2 9.4 - - - +
247A ARG* 3.4 31.9 - - + +
248A GLU* 1.3 74.9 - - - +
250A ASP* 1.3 62.1 + - - +
268A ASN* 3.5 0.2 - - - -
269A PHE* 2.9 24.8 + - - +
270A LYS* 2.9 48.9 + - + +
272A ARG* 4.1 16.6 - - - +
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Residues in contact with ASP 250 (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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77A TYR* 3.3 7.7 - - - -
78A TRP* 2.9 54.9 + - + +
80A ALA* 3.3 13.2 - - - +
181A ARG* 2.7 45.6 + - - +
248A GLU 4.1 0.4 + - - -
249A MET* 1.3 73.1 - - - +
251A LEU* 1.3 59.8 + - - +
252A TYR 3.7 0.2 - - - -
265A ASN* 2.8 27.1 + - - +
266A TYR 3.2 10.1 - - - +
267A LYS* 3.7 3.3 - - - -
268A ASN 2.9 8.3 + - - -
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Residues in contact with LEU 251 (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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75A LYS* 3.5 32.8 - - + +
76A LEU 3.5 15.7 - - - +
77A TYR* 3.5 34.5 - - + +
249A MET 4.1 0.8 + - - -
250A ASP* 1.3 71.9 - - - +
252A TYR* 1.3 57.0 + - - +
253A GLN* 4.2 20.4 - - - +
264A ALA 3.5 2.4 - - - +
265A ASN* 3.4 2.9 - - - -
266A TYR* 2.8 53.0 + - + -
269A PHE* 3.7 33.8 - - + +
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Residues in contact with TYR 252 (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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75A LYS* 3.2 1.7 - - - -
76A LEU* 2.8 53.0 + - + -
78A TRP* 3.7 6.1 - - - +
190A ASN* 2.6 36.1 + - + -
191A GLU* 3.5 3.6 - - - -
192A LEU* 3.8 20.2 - - + -
193A PHE* 3.4 35.8 + + + -
194A LEU* 3.4 19.8 + - - +
207A PHE* 3.7 14.5 - + - -
250A ASP 3.6 1.0 + - - -
251A LEU* 1.3 71.4 - - - +
253A GLN* 1.3 59.9 + - - +
254A ILE* 3.6 22.4 - - + +
263A GLY* 3.8 4.4 - - - -
264A ALA 3.5 10.1 - - - -
265A ASN* 3.7 20.6 - - + +
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Residues in contact with GLN 253 (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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73A PHE* 3.3 32.8 - - + -
74A SER 3.2 13.7 - - - +
75A LYS* 3.7 8.4 - - + +
207A PHE* 4.7 0.2 - - - -
251A LEU* 4.2 17.6 - - - +
252A TYR* 1.3 77.0 - - - +
254A ILE* 1.3 65.6 + - - +
255A ARG* 4.0 10.9 + - - -
262A ALA 3.8 0.2 - - - +
263A GLY* 3.1 3.6 - - - -
264A ALA* 2.7 56.3 + - + +
266A TYR* 3.6 32.3 + - + -
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Residues in contact with ILE 254 (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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73A PHE* 3.4 4.6 - - - -
74A SER* 2.9 33.7 + - - +
194A LEU* 3.8 23.1 - - + -
203A ALA* 3.2 26.0 - - - +
206A ASN* 3.5 30.3 - - + +
207A PHE* 3.5 20.9 - - + -
252A TYR* 3.6 27.8 - - + +
253A GLN* 1.3 80.3 - - - +
255A ARG* 1.3 64.5 + - - +
261A TRP* 4.2 10.8 - - + -
262A ALA 3.2 6.5 - - - +
263A GLY* 4.1 4.3 - - - -
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Residues in contact with ARG 255 (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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72A ASP* 3.2 10.1 - - + +
73A PHE* 3.5 44.2 - - + +
253A GLN* 4.0 13.3 + - - -
254A ILE* 1.3 78.3 - - - +
256A TRP* 1.3 74.4 + - - +
257A ASN* 3.9 6.0 + - + +
260A TYR 3.7 1.2 - - - +
261A TRP* 3.4 7.9 - - - -
262A ALA* 3.0 34.9 + - + +
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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