Contacts of the helix formed by residues 314 - 325 (chain B) in PDB entry 2CT8
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 314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A GLU* 3.4 13.5 - - - -
310B VAL* 2.8 25.0 + - - -
312B GLU 3.9 0.2 - - - -
313B TYR* 1.3 72.2 - - - +
315B LEU* 1.3 66.3 + - - -
316B ASP 3.6 1.8 - - - -
317B GLU* 3.3 10.2 + - - -
318B VAL* 2.9 26.2 + - - +
495B ARG* 3.9 8.2 - - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLU* 3.3 16.8 + - - +
29B ILE* 5.6 1.3 - - + -
86B PHE 4.5 4.5 - - - +
87B LEU* 3.3 58.8 - - + +
88B LYS* 4.0 13.2 - - + -
310B VAL* 3.6 22.2 - - + +
314B GLY* 1.3 73.3 - - - +
316B ASP* 1.3 60.1 + - - +
317B GLU* 4.1 0.4 + - - -
318B VAL* 3.2 4.4 + - + +
319B ARG* 2.9 42.1 + - + +
457B ASN* 3.1 28.7 - - - +
458B LYS* 6.2 0.2 - - - +
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Residues in contact with ASP 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLY 3.6 0.2 - - - -
315B LEU* 1.3 77.8 - - - +
317B GLU* 1.3 64.4 + - - +
319B ARG* 3.6 8.5 - - - +
320B TYR* 2.7 32.4 + - - +
347B LEU* 5.1 0.7 - - - -
455B THR* 3.4 35.5 - - + +
456B PRO* 3.5 3.5 - - - +
457B ASN* 2.9 41.8 + - - +
458B LYS* 3.0 38.4 - - + +
492B PHE* 4.6 1.6 - - + -
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B TYR* 3.2 28.8 - - + +
314B GLY* 3.5 12.9 - - - +
315B LEU 3.2 0.6 + - - -
316B ASP* 1.3 78.3 + - - +
318B VAL* 1.3 57.7 + - - +
320B TYR* 3.4 3.6 - - - +
321B PHE* 3.0 25.5 + - - +
339B ILE* 5.4 0.4 - - - -
343B ILE* 3.8 30.8 - - + +
347B LEU* 3.8 24.9 - - + +
458B LYS* 3.6 27.5 + - - -
492B PHE* 3.9 19.2 - - + +
493B PRO* 4.3 15.9 - - - +
495B ARG* 4.3 6.0 + - - -
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 5.3 4.5 - - + -
29B ILE* 5.9 2.7 - - + -
309B VAL* 4.2 21.5 - - + +
310B VAL* 4.4 16.4 - - + -
313B TYR* 4.2 15.7 - - + -
314B GLY 2.9 20.6 + - - +
315B LEU* 3.9 5.2 - - + +
317B GLU* 1.3 72.5 - - - +
319B ARG* 1.3 74.7 + - + +
321B PHE* 4.2 6.5 - - - -
322B LEU* 3.0 43.2 + - + +
334B PHE* 5.0 13.2 - - + -
339B ILE* 5.1 3.1 - - + -
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Residues in contact with ARG 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 4.0 33.1 + - + +
32B ASP* 2.6 35.1 + - - +
33B THR* 3.6 18.0 - - - +
36B ARG* 4.0 0.6 - - - +
87B LEU 4.1 14.3 + - - -
88B LYS* 4.7 3.8 + - - +
89B ILE* 4.3 6.3 - - - +
315B LEU* 2.9 33.5 + - + +
316B ASP* 3.6 18.6 - - - +
318B VAL* 1.3 81.8 - - + +
320B TYR* 1.3 65.6 + - - +
322B LEU* 3.4 3.9 + - - +
323B LEU* 3.3 24.9 + - + +
453B PRO 3.3 22.2 + - - -
454B ILE* 3.1 19.4 + - - +
456B PRO* 3.7 15.8 - - - +
457B ASN* 5.2 1.2 - - - +
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Residues in contact with TYR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ASP 2.7 20.8 + - - +
317B GLU 3.4 4.0 - - - +
319B ARG* 1.3 73.4 - - - +
321B PHE* 1.3 67.0 + - - +
323B LEU* 3.1 4.0 + - - +
324B ARG* 2.9 38.1 + - + +
342B ARG* 4.4 13.5 - - + -
343B ILE* 6.3 0.2 - - + -
346B GLU* 3.1 28.2 + - + +
347B LEU* 3.5 46.4 - - + -
351B ILE* 4.7 3.5 - - + +
402B ILE* 3.7 21.8 - - + +
405B ILE* 6.0 0.2 - - + -
406B LEU* 3.5 23.9 - - - +
451B LEU* 4.6 11.7 - - + -
454B ILE* 3.0 32.3 - - + +
455B THR* 4.0 4.7 - - + -
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Residues in contact with PHE 321 (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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289B TRP* 4.0 13.2 - + - -
317B GLU 3.0 17.8 + - - +
318B VAL* 3.2 4.9 + - - +
320B TYR* 1.3 82.6 - - + +
322B LEU* 1.3 61.5 + - - +
324B ARG* 4.5 1.1 - - - +
325B GLU* 2.9 72.2 + - + +
333B ASP 4.1 4.7 - - - -
334B PHE* 3.5 42.2 - + - -
335B SER 4.7 0.4 - - - -
338B ALA* 3.4 24.2 - - + -
339B ILE* 3.4 40.8 - - + -
342B ARG* 3.7 15.9 - - + -
343B ILE* 6.2 0.4 - - + -
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.0 24.0 - - + -
25B ALA* 6.0 0.4 - - + -
26B TYR* 3.4 40.1 + - + -
29B ILE* 4.6 19.1 - - + -
289B TRP* 3.5 39.7 - - + +
318B VAL* 3.0 37.7 + - + +
319B ARG* 3.8 4.0 - - - +
321B PHE* 1.3 75.9 - - - +
323B LEU* 1.3 62.4 + - + +
325B GLU 4.8 0.9 + - - -
326B VAL 5.0 4.0 - - - +
334B PHE* 3.9 27.8 - - + -
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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
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26B TYR* 4.4 10.3 - - + -
29B ILE* 4.2 10.1 - - + -
30B ALA* 4.2 17.0 - - + +
33B THR* 3.4 33.9 - - + +
319B ARG 3.3 15.5 + - - +
320B TYR 3.1 3.7 + - - +
322B LEU* 1.3 82.6 - - + +
324B ARG* 1.3 60.4 + - - +
326B VAL 4.4 6.9 - - - +
328B PHE* 4.9 2.2 - - + -
398B PHE* 3.7 47.8 - - + +
399B TYR* 3.9 7.3 + - - -
402B ILE* 3.2 20.6 - - + +
454B ILE* 4.3 17.5 - - + +
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Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B TYR* 2.9 29.1 + - + +
321B PHE* 4.4 0.9 - - - +
323B LEU* 1.3 79.7 - - - +
325B GLU* 1.3 68.6 + - - +
326B VAL 3.3 2.2 - - - -
342B ARG* 2.9 55.7 - - - +
346B GLU* 2.9 29.1 + - - -
399B TYR* 3.1 32.4 + - + +
402B ILE* 3.4 36.6 - - + -
406B LEU* 4.9 6.2 - - + +
24D G 4.1 6.7 + - - -
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Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B TRP* 4.0 12.1 - - + -
321B PHE* 2.9 49.5 + - + +
324B ARG* 1.3 83.0 + - - +
326B VAL* 1.3 73.2 + - + +
327B PRO* 4.5 0.7 - - - +
333B ASP 4.7 4.7 - - - +
338B ALA* 3.9 14.2 - - - +
342B ARG* 3.1 33.9 + - - +
399B TYR* 3.7 9.2 + - - -
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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