Contacts of the helix formed by residues 302 - 321 (chain B) in PDB entry 4KMR
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 GLY 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B GLU* 3.0 15.5 + - - -
301B PRO* 1.3 81.3 - - - +
303B ARG* 1.3 62.5 + - - +
304B HIS 3.3 2.9 - - - -
305B ASP* 3.1 8.9 + - - +
306B ILE* 2.9 32.4 + - - +
333B PRO* 4.1 3.3 - - - +
334B GLU 3.7 12.3 - - - -
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 5.2 12.3 - - + -
85B GLN* 4.3 39.3 + - - +
86B LEU* 4.1 14.6 - - + +
89B GLU* 4.6 10.5 - - + +
284B ASP 4.8 1.8 + - - -
285B ASP* 4.0 22.6 + - - +
290B ARG* 5.6 5.9 - - - +
300B GLU* 2.9 41.5 + - - +
301B PRO* 4.0 0.6 - - - +
302B GLY* 1.3 71.2 - - - +
304B HIS* 1.4 87.3 + - + +
306B ILE* 3.6 12.4 - - + +
307B ALA* 3.0 31.7 + - - +
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Residues in contact with HIS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 3.4 37.3 + - + +
92B ARG* 5.0 3.1 - - - -
93B VAL* 5.4 0.2 - - - +
300B GLU* 5.1 5.6 + - - -
302B GLY 3.3 0.8 - - - -
303B ARG* 1.4 110.2 + - - +
305B ASP* 1.3 57.8 + - - +
307B ALA* 3.5 1.6 + - - +
308B ARG* 3.0 31.4 + - - +
336B ARG* 5.9 2.7 + - - -
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Residues in contact with ASP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLY* 3.1 9.8 + - - +
304B HIS* 1.3 75.0 - - - +
306B ILE* 1.3 66.1 + - - +
308B ARG* 4.5 4.4 - - - +
309B ALA* 2.8 36.2 + - - +
331B THR* 4.7 5.9 - - - +
332B ALA 5.1 0.2 - - - -
333B PRO* 3.5 31.8 - - + +
334B GLU* 4.5 3.3 + - - +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE* 5.0 7.2 - - + -
86B LEU* 3.9 17.0 - - + -
152B LEU* 4.0 27.1 - - + -
164B VAL* 4.1 17.6 - - + +
166B MSE 3.8 33.4 - - + -
301B PRO* 4.1 7.2 - - + +
302B GLY 2.9 29.2 + - - +
303B ARG* 3.6 9.2 - - - +
305B ASP* 1.3 75.7 - - - +
307B ALA* 1.3 64.3 + - - +
309B ALA* 4.1 0.7 - - - +
310B ALA* 3.0 29.7 + - + +
333B PRO* 3.7 17.5 - - + +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 4.4 2.7 - - + -
89B GLU* 3.8 29.6 - - + +
90B VAL* 3.8 26.7 - - + +
93B VAL* 4.5 4.5 - - + -
303B ARG 3.0 17.0 + - - +
304B HIS 4.0 2.7 - - - +
306B ILE* 1.3 80.6 - - - +
308B ARG* 1.3 62.3 + - - +
310B ALA* 4.0 1.9 - - - +
311B VAL* 3.1 29.7 + - - +
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Residues in contact with ARG 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 5.3 0.4 + - - -
92B ARG* 3.8 21.0 - - - +
93B VAL* 3.8 28.4 - - + +
96B GLU* 3.1 28.3 + - - -
97B GLN* 4.3 8.7 - - - +
304B HIS 3.0 18.5 + - - +
305B ASP* 4.2 4.9 - - - +
307B ALA* 1.3 77.9 - - - +
309B ALA* 1.3 64.0 + - - +
311B VAL* 4.1 0.2 - - - -
312B THR* 2.7 40.0 + - - +
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B VAL* 4.3 8.3 - - + -
305B ASP* 2.8 34.5 + - - +
306B ILE* 4.1 2.2 - - - +
308B ARG* 1.3 73.2 - - - +
310B ALA* 1.3 57.1 + - - +
312B THR* 3.9 3.0 - - - -
313B MSE 2.9 43.8 + - + +
331B THR* 4.1 22.7 - - + +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 5.8 1.8 - - + -
129B LEU* 3.6 26.4 - - + +
150B VAL* 3.9 20.4 - - + +
152B LEU* 6.5 1.1 - - + -
164B VAL* 4.4 6.0 - - + +
306B ILE* 3.0 21.8 + - + +
307B ALA* 4.0 4.0 - - - +
309B ALA* 1.3 78.3 - - - +
311B VAL* 1.3 62.6 + - - +
313B MSE 4.4 1.1 - - - -
314B LEU* 3.0 25.8 + - - +
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 4.4 5.4 - - + -
90B VAL* 3.9 38.1 - - + +
93B VAL* 3.7 20.0 - - + -
94B ALA* 4.1 7.9 - - + +
97B GLN* 3.6 17.3 - - - +
99B LEU* 3.9 20.5 - - + +
129B LEU* 4.0 9.2 - - + -
307B ALA 3.1 18.0 + - - +
310B ALA* 1.3 75.5 - - - +
312B THR* 1.3 65.1 + - - +
314B LEU* 3.3 6.5 + - - +
315B SER* 3.0 22.2 + - - -
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Residues in contact with THR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLN* 3.2 26.9 + - - +
308B ARG* 2.7 32.4 + - - +
309B ALA* 4.0 3.6 - - - -
311B VAL* 1.3 78.7 - - - +
313B MSE 1.3 63.9 + - + +
315B SER* 3.3 5.4 + - - -
316B GLU* 3.0 35.9 + - + +
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Residues in contact with MSE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B VAL* 4.1 8.5 - - + -
162B ASP* 3.7 25.1 - - + +
163B HIS 4.6 1.6 - - - +
164B VAL* 3.5 32.3 - - + -
309B ALA* 2.9 26.3 + - + +
310B ALA 4.0 1.8 - - - +
312B THR* 1.3 77.3 - - + +
314B LEU* 1.3 61.9 + - - +
316B GLU* 3.2 9.9 + - - +
317B ARG* 3.1 26.4 + - - +
329B ARG* 3.6 46.4 + - - +
331B THR* 3.8 19.7 - - - +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.6 24.5 - - + -
99B LEU* 6.4 0.4 - - + -
127B GLY* 3.5 26.7 - - - -
128B LEU 3.5 11.0 - - - +
129B LEU* 3.8 22.9 - - + -
148B PRO* 3.5 42.4 - - + +
149B LEU 3.8 2.7 - - - +
150B VAL* 4.0 11.5 - - + +
310B ALA 3.0 18.5 + - - +
311B VAL* 3.8 5.2 - - + +
313B MSE 1.3 72.1 - - - +
315B SER* 1.3 66.3 + - - +
317B ARG* 3.1 6.4 + - + +
318B ILE* 2.9 32.2 + - + +
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLN* 3.1 24.4 + - - +
99B LEU* 3.6 19.8 - - - +
311B VAL 3.0 11.1 + - - -
312B THR* 3.5 9.6 - - - -
314B LEU* 1.3 74.8 - - - +
316B GLU* 1.3 62.7 + - - +
318B ILE* 3.6 11.8 + - - +
319B ALA* 3.2 22.5 + - - +
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B THR* 3.0 33.6 + - + +
313B MSE 3.2 9.9 + - - +
315B SER* 1.3 77.5 - - - +
317B ARG* 1.3 61.8 + - - +
319B ALA* 3.4 6.7 + - - +
320B ASP* 3.2 26.0 + - - +
326B ILE* 4.1 18.1 - - + +
329B ARG* 2.4 38.7 + - - +
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PRO* 3.5 30.8 - - + +
149B LEU 5.2 4.7 + - - +
150B VAL* 5.3 0.4 - - + -
160B PRO* 3.6 37.8 + - - +
162B ASP* 2.8 38.7 + - - +
313B MSE 3.1 15.1 + - - +
314B LEU* 3.6 6.5 - - + +
316B GLU* 1.3 73.1 - - - +
318B ILE* 1.3 65.2 + - - +
320B ASP* 3.2 18.1 + - - +
321B ALA* 3.2 10.4 + - - -
322B GLY 4.4 2.6 + - - -
324B GLY* 4.3 7.5 - - - -
326B ILE* 3.0 35.8 + - - +
327B GLU 3.2 24.0 + - - -
328B PRO* 3.7 5.1 - - - +
329B ARG* 4.0 3.6 - - - +
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 4.0 21.1 - - + -
99B LEU* 5.3 7.6 - - + -
126B ASP* 3.4 52.5 - - + +
127B GLY 4.1 0.7 - - - +
148B PRO* 3.8 12.1 - - + +
314B LEU* 2.9 27.8 + - + +
315B SER* 3.7 9.9 - - - +
317B ARG* 1.3 75.5 - - - +
319B ALA* 1.3 63.8 + - - +
321B ALA* 3.2 15.2 + - - +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B SER 3.2 11.2 + - - +
316B GLU* 3.7 9.6 - - - +
317B ARG 3.3 0.2 - - - -
318B ILE* 1.3 80.7 - - - +
320B ASP* 1.3 66.2 + - - +
321B ALA* 3.5 4.3 + - - +
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Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B GLU 3.2 13.0 + - - +
317B ARG* 3.2 13.6 + - - +
318B ILE 3.2 1.2 - - - -
319B ALA* 1.3 81.1 - - - +
321B ALA* 1.3 70.4 + - - +
322B GLY 3.2 2.9 + - - +
323B THR* 3.5 36.5 + - - +
324B GLY 5.3 1.8 - - - +
325B ALA* 4.5 5.8 + - - +
326B ILE* 3.4 30.8 + - - +
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLY 5.8 1.1 - - - -
148B PRO* 6.1 1.8 - - - -
317B ARG 3.2 5.1 + - - -
318B ILE 3.2 14.6 + - - +
319B ALA 4.4 4.0 - - - +
320B ASP* 1.3 78.4 - - - +
322B GLY* 1.3 58.8 + - - +
323B THR* 3.7 1.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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