Contacts of the helix formed by residues 311 - 329 (chain B) in PDB entry 7CE1
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 ASP 311 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B HIS* 5.5 0.2 + - - -
294B SER 4.5 2.6 - - - +
309B ASN* 3.7 8.4 + - + +
310B GLU* 1.3 71.7 - - - +
312B ILE* 1.3 60.7 + - - +
313B LYS* 3.5 13.5 + - - +
314B LEU* 3.2 40.7 + - + +
315B ALA* 3.1 22.3 + - - +
317B ARG* 4.7 7.8 + - - -
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU* 5.7 0.2 - - - +
92B GLY* 3.2 25.1 - - - +
93B PHE* 4.1 8.7 - - + +
94B THR* 5.4 0.7 - - - -
96B GLN* 4.6 3.6 - - + +
97B MET* 3.5 34.6 - - + +
164B HIS* 4.8 12.6 - - + +
294B SER* 3.4 30.7 + - - +
310B GLU* 3.0 29.7 + - + +
311B ASP* 1.3 70.2 + - - +
313B LYS* 1.3 54.3 + - - +
314B LEU 3.1 0.9 - - - -
315B ALA* 3.0 9.2 + - + +
316B GLY* 2.6 31.2 + - - -
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Residues in contact with LYS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 4.6 16.0 - - - +
96B GLN* 2.9 51.5 + - - +
97B MET* 4.1 0.2 - - - +
99B PHE* 4.9 2.4 - - + +
100B GLY* 3.4 8.5 - - - +
103B GLU* 3.1 29.1 + - - +
311B ASP* 3.5 12.7 + - - +
312B ILE* 1.3 75.5 - - - +
314B LEU* 1.3 62.2 + - - +
316B GLY 3.9 1.6 - - - +
317B ARG* 2.9 46.5 + - - +
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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
----------------------------------------------------------
176B HIS* 4.7 6.8 + - + +
311B ASP* 3.2 40.0 + - + +
312B ILE 3.1 0.2 - - - -
313B LYS* 1.3 81.9 - - - +
315B ALA* 1.3 62.4 + - - +
317B ARG* 3.5 37.0 + - + +
318B GLU* 3.5 21.8 + - + +
339B SER* 4.8 18.6 - - - -
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 5.6 0.4 - - + -
164B HIS* 3.7 23.8 - - + +
176B HIS* 3.5 33.0 - - + +
310B GLU* 6.1 2.5 - - + -
311B ASP 3.1 10.1 + - - +
312B ILE* 3.0 18.6 + - + +
314B LEU* 1.3 77.4 - - - +
316B GLY* 1.3 60.9 + - - +
317B ARG 3.4 0.2 + - - -
318B GLU* 3.4 1.4 + - - -
319B LEU* 3.0 31.4 + - + +
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Residues in contact with GLY 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 3.6 29.6 - - - +
100B GLY 3.5 6.5 - - - -
101B ILE* 3.3 15.9 - - - +
312B ILE 2.6 16.7 + - - -
313B LYS 3.2 5.9 + - - -
315B ALA* 1.3 74.0 - - - +
317B ARG* 1.3 60.1 + - - +
319B LEU* 4.0 2.9 - - - +
320B ALA* 3.2 17.3 + - - +
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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
----------------------------------------------------------
100B GLY* 3.2 20.2 - - - +
103B GLU* 4.4 22.2 + - - -
104B VAL* 3.1 26.3 - - + +
311B ASP* 4.7 10.5 + - - -
313B LYS* 2.9 28.5 + - - +
314B LEU* 3.5 27.5 + - + +
315B ALA 3.3 0.4 - - - -
316B GLY* 1.3 77.2 - - - +
318B GLU* 1.3 52.6 + - + +
320B ALA* 3.2 0.7 - - - +
321B LYS* 2.7 29.4 + - - +
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B HIS* 5.0 16.8 + - + +
314B LEU* 3.5 20.1 + - + +
315B ALA 3.4 3.3 + - - +
316B GLY 3.4 0.2 - - - -
317B ARG* 1.3 77.6 - - + +
319B LEU* 1.3 57.9 + - - +
320B ALA 3.1 0.9 - - - -
321B LYS* 3.7 15.8 - - + +
322B ALA* 2.7 35.4 + - + +
337B SER* 5.0 16.0 + - - +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 3.8 29.4 - - + -
101B ILE* 5.3 1.6 - - + -
140B ILE* 4.4 17.9 - - + -
162B VAL* 3.4 25.1 - - + +
163B THR 3.4 34.3 - - - +
164B HIS* 3.8 17.7 - - + +
176B HIS* 4.1 16.9 - - + +
315B ALA 3.0 28.1 + - - +
316B GLY* 4.0 5.2 - - - +
318B GLU* 1.3 76.8 - - - +
320B ALA* 1.3 62.2 + - - +
322B ALA* 3.7 3.3 - - - +
323B LEU* 3.0 25.8 + - - +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 3.8 13.0 - - + +
104B VAL* 3.7 22.0 - - + -
105B LEU* 3.7 18.4 - - + -
140B ILE* 5.0 4.2 - - - +
316B GLY 3.2 13.1 + - - +
317B ARG 3.2 10.1 - - - +
319B LEU* 1.3 79.7 - - - +
321B LYS* 1.3 62.4 + - - +
323B LEU* 3.2 5.9 + - - +
324B LEU* 3.1 27.7 + - - +
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 4.1 13.4 - - + +
317B ARG 2.7 19.3 + - - +
318B GLU* 3.4 19.9 + - + +
320B ALA* 1.3 73.8 - - - +
322B ALA* 1.3 62.5 + - - +
324B LEU* 3.8 6.1 + - - +
325B ALA* 3.5 18.7 + - - +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B VAL* 4.0 16.8 - - + -
174B ALA* 4.4 4.3 - - + -
175B TYR 5.3 1.3 - - - +
176B HIS* 6.3 0.2 - - + -
318B GLU* 2.7 24.1 + - + +
319B LEU 3.7 4.0 - - - +
321B LYS* 1.3 72.3 - - - +
323B LEU* 1.3 65.5 + - - +
325B ALA* 3.1 5.4 + - - +
326B ARG 3.0 18.5 + - - -
335B LEU* 3.1 40.5 - - + +
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 3.9 16.4 - - + -
138B GLY* 3.8 7.6 - - - -
139B VAL 3.6 27.4 - - - +
140B ILE* 3.6 21.1 - - + -
160B PRO* 3.8 9.9 - - + +
161B PHE* 3.5 39.3 - - - +
162B VAL* 3.7 7.2 - - + +
319B LEU 3.0 17.8 + - - +
320B ALA* 3.8 4.3 - - - +
322B ALA* 1.3 76.4 - - - +
324B LEU* 1.3 57.6 + - - +
326B ARG* 3.3 4.5 + - + +
327B ILE* 2.9 42.3 + - + +
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Residues in contact with LEU 324 (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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80B ILE* 4.9 9.4 - - + -
104B VAL* 3.9 27.6 - - + +
105B LEU* 5.0 8.7 - - + -
108B THR* 4.2 22.7 - - + +
110B TYR* 3.9 42.0 - - + +
320B ALA 3.1 16.6 + - - +
321B LYS* 4.0 6.1 - - - +
322B ALA 3.2 0.2 - - - -
323B LEU* 1.3 74.5 - - - +
325B ALA* 1.3 64.6 + - - +
327B ILE* 3.1 6.8 + - + +
328B ASN* 3.0 30.5 + - - +
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Residues in contact with ALA 325 (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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321B LYS 3.5 10.3 + - - +
322B ALA* 3.1 10.4 + - - +
324B LEU* 1.3 78.9 - - - +
326B ARG* 1.3 56.5 + - - +
328B ASN* 3.4 8.5 + - - +
329B GLY 3.0 8.0 + - - -
330B ALA* 2.8 34.3 + - + +
335B LEU* 3.7 20.4 - - + -
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Residues in contact with ARG 326 (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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155B THR* 5.5 9.7 - - - +
159B MET 5.4 2.2 + - - -
160B PRO* 4.0 23.4 - - + +
161B PHE* 4.1 32.0 + - - +
172B GLU 5.4 2.0 + - - -
173B HIS* 5.4 2.6 - - - +
174B ALA* 4.2 8.7 - - + +
322B ALA 3.0 7.1 + - - +
323B LEU* 3.7 11.7 - - + +
325B ALA* 1.3 76.2 - - - +
327B ILE* 1.3 61.5 + - - +
329B GLY* 3.1 18.0 + - - -
330B ALA 3.7 13.8 + - - +
332B PRO* 3.5 40.3 - - - +
335B LEU* 3.3 24.2 - - + +
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Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 5.0 4.7 - - - -
80B ILE* 3.5 31.0 - - + -
110B TYR* 3.7 25.1 - - + +
137B ASP* 3.2 38.6 - - + +
138B GLY* 3.7 3.4 - - - -
160B PRO* 3.7 19.5 - - + +
323B LEU* 2.9 23.4 + - + +
324B LEU* 3.1 7.4 + - + +
326B ARG* 1.3 74.2 - - - +
328B ASN* 1.3 67.1 + - - +
329B GLY* 3.3 1.0 + - - -
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Residues in contact with ASN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 5.7 0.3 + - - -
110B TYR* 4.5 6.8 + - - -
324B LEU* 3.0 17.1 + - - +
325B ALA* 3.8 10.4 - - - +
327B ILE* 1.3 83.0 - - - +
329B GLY* 1.3 58.6 + - - +
330B ALA* 5.0 0.7 - - + +
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Residues in contact with GLY 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ALA 3.0 2.0 + - - -
326B ARG* 3.1 14.4 + - - -
327B ILE 4.2 0.9 - - - -
328B ASN* 1.3 80.7 - - - +
330B ALA* 1.3 68.3 + - - +
331B PRO* 3.7 2.8 - - - +
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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