Contacts of the strand formed by residues 236 - 248 (chain A) in PDB entry 3K3B
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 HIS 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A LEU 3.7 0.7 - - - +
162A GLU* 3.0 10.4 - - - +
163A ILE* 2.8 58.1 + - + +
235A SER* 1.3 73.2 - - - +
237A SER* 1.3 59.9 + - - +
238A VAL* 4.9 0.9 - - + -
264A VAL* 4.9 2.7 - - + -
265A ASP 3.6 4.5 - - - +
266A LEU* 3.4 24.0 - - + +
267A ALA* 3.0 41.0 + - + +
288A ILE* 4.8 5.7 - - + +
291A SER* 2.8 28.1 + - - -
292A LEU* 4.0 12.1 - - + -
316A LEU* 4.2 27.9 - - + +
372A NO3 4.5 3.6 + - - -
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Residues in contact with SER 237 (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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116A GLU* 4.4 2.1 + - - -
160A LEU* 3.3 11.8 - - - +
161A LEU 3.7 3.8 - - - -
162A GLU* 4.2 2.2 - - - -
221A ARG* 3.0 42.3 + - - -
235A SER 3.9 1.1 + - - -
236A HIS* 1.3 72.2 - - - +
238A VAL* 1.3 61.7 + - - +
239A PHE* 3.9 1.6 + - - +
263A LEU 3.6 1.9 + - - +
264A VAL* 3.2 7.6 - - - +
265A ASP* 2.9 54.1 + - - +
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER* 3.7 1.7 + - - +
160A LEU* 3.4 6.3 - - - -
161A LEU* 2.8 59.0 + - + +
163A ILE* 4.8 4.7 - - + -
236A HIS 4.9 1.3 - - - -
237A SER* 1.3 77.6 + - - +
239A PHE* 1.3 59.3 + - - +
240A SER* 3.7 18.9 + - - +
262A ASN* 4.5 4.0 - - + -
263A LEU 4.2 1.3 - - - -
264A VAL* 4.3 13.0 - - + +
316A LEU* 4.3 23.8 - - + -
319A ILE* 5.0 9.6 - - + -
320A LEU* 4.1 22.9 - - + -
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Residues in contact with PHE 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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136A ILE* 3.7 34.5 - - + -
140A LEU* 4.0 13.2 - - + -
158A VAL* 3.7 44.0 - - + -
159A SER 3.5 3.8 - - - -
160A LEU* 3.9 27.7 - - + +
172A LEU* 4.9 4.5 - - + -
213A ILE* 5.7 1.8 - - + -
214A LEU* 3.7 31.0 - - + -
237A SER* 3.9 1.3 - - - +
238A VAL* 1.3 71.7 - - - +
240A SER* 1.3 65.1 + - - +
241A VAL* 4.5 2.9 - - + -
261A LEU 3.6 1.9 - - - +
262A ASN* 3.5 1.5 - - - -
263A LEU* 2.8 47.4 + - + +
371A L31 4.0 15.7 - + + -
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Residues in contact with SER 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LYS 3.9 0.2 - - - +
158A VAL* 3.1 8.0 - - - +
159A SER* 2.9 49.8 + - - +
238A VAL* 3.7 12.3 + - - +
239A PHE* 1.3 74.5 - - - +
241A VAL* 1.3 59.8 + - - +
242A THR* 4.2 0.7 - - - -
260A LYS* 3.7 18.5 + - - -
261A LEU 3.5 4.7 - - - -
262A ASN* 2.6 24.8 + - - -
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Residues in contact with VAL 241 (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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139A THR* 4.9 1.6 - - + -
140A LEU* 4.0 11.2 - - + -
143A ILE* 3.8 31.2 - - + -
156A VAL* 3.8 23.6 - - + -
157A LYS 3.4 3.4 - - - +
158A VAL* 3.9 9.6 - - + -
239A PHE* 4.5 2.7 - - + -
240A SER* 1.3 74.9 - - - +
242A THR* 1.3 61.4 + - - +
243A ILE* 4.1 9.1 + - + +
259A GLY 4.0 0.3 - - - +
260A LYS* 3.4 5.3 - - - +
261A LEU* 3.0 55.4 + - + +
263A LEU* 4.6 12.3 - - + -
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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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155A SER 3.5 3.8 - - - +
156A VAL* 3.6 2.1 - - - -
157A LYS* 2.8 52.8 + - - +
201A GLU* 4.7 4.3 + - - -
240A SER 5.2 0.3 - - - -
241A VAL* 1.3 72.6 - - - +
243A ILE* 1.3 63.6 + - - +
244A HIS* 4.1 16.2 + - + -
258A ILE* 3.8 25.8 - - + -
259A GLY 3.5 4.9 - - - +
260A LYS* 2.8 32.9 + - + +
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Residues in contact with ILE 243 (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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90A LEU* 4.8 0.7 - - + -
93A VAL* 4.0 23.8 - - + -
94A ILE* 4.7 12.6 - - + -
143A ILE* 3.5 39.9 - - + -
147A LEU* 3.6 26.2 - - + -
154A PHE* 4.2 3.8 - - + -
155A SER 3.5 8.7 - - - +
156A VAL* 4.3 4.5 - - + -
241A VAL* 4.1 13.5 - - + +
242A THR* 1.3 76.5 - - - +
244A HIS* 1.3 66.8 + - - +
245A MET* 3.7 15.1 + - + +
257A LYS 3.8 0.3 - - - +
258A ILE* 3.2 7.3 - - - +
259A GLY* 2.8 36.3 + - - +
261A LEU* 6.4 0.2 - - + -
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Residues in contact with HIS 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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153A GLU 3.6 0.7 - - - +
154A PHE* 2.9 28.8 - - - +
155A SER* 3.0 30.2 + - - +
157A LYS* 4.2 22.8 - - - +
242A THR* 4.1 21.8 + - + +
243A ILE* 1.3 73.9 - - - +
245A MET* 1.3 60.0 + - - +
246A LYS 4.3 0.2 - - - -
256A VAL* 6.4 1.3 - - + -
257A LYS 3.8 2.5 - - - -
258A ILE* 3.6 31.6 - - + +
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Residues in contact with MET 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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93A VAL 3.8 0.7 - - - +
94A ILE* 3.0 50.9 - - - +
96A GLY 4.2 0.2 - - - +
147A LEU* 3.8 26.7 - - + -
152A THR* 3.7 13.5 - - + -
153A GLU 3.4 3.1 - - - -
154A PHE* 4.2 0.4 - - + -
243A ILE* 3.7 19.1 - - + +
244A HIS* 1.3 78.4 - - - +
246A LYS* 1.3 59.4 + - - +
255A LEU 3.4 1.7 - - - +
256A VAL* 3.3 8.4 - - - +
257A LYS* 2.8 61.8 + - + +
259A GLY* 3.7 26.7 - - - +
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Residues in contact with LYS 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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151A GLY 5.0 0.3 - - - +
152A THR* 3.3 2.5 - - - +
153A GLU* 2.7 66.3 + - + +
245A MET* 1.3 74.1 - - - +
247A GLU* 1.3 59.2 + - - +
248A THR* 4.3 4.6 + - - +
254A GLU* 3.3 36.9 + - - +
255A LEU 3.4 1.1 - - - -
256A VAL* 3.5 28.9 - - + +
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Residues in contact with GLU 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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150A ASN* 5.3 8.3 + - - +
151A GLY 5.8 0.2 - - - -
152A THR* 4.3 23.5 + - + +
246A LYS* 1.3 73.3 - - - +
248A THR* 1.3 66.2 + - - +
249A THR* 5.4 4.3 - - - +
253A GLU 3.5 3.2 - - - +
254A GLU* 3.4 5.9 - - - +
255A LEU* 2.9 57.7 + - + +
257A LYS* 2.8 34.4 + - - -
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Residues in contact with THR 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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151A GLY 5.7 2.6 + - - -
246A LYS* 4.2 5.4 + - - +
247A GLU* 1.3 77.8 + - - +
249A THR* 1.3 74.6 + - - +
250A ILE* 5.0 5.2 - - + +
253A GLU 3.8 1.8 - - - -
254A GLU* 2.8 37.0 + - + -
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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