Contacts of the helix formed by residues 340 - 359 (chain B) in PDB entry 1EBF
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 340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL* 5.4 1.1 - - - -
339B ALA* 1.3 77.9 - - - +
341B ALA* 1.3 65.2 - - - -
342B ALA 3.4 2.4 + - - -
343B VAL* 3.5 4.7 + - - -
344B THR* 2.6 33.3 + - - -
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Residues in contact with ALA 341 (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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15B VAL* 3.4 44.8 - - + +
16B VAL* 4.5 9.0 - - - +
19B ALA* 3.9 9.1 - - + +
340B GLY* 1.3 71.2 - - - +
342B ALA* 1.3 59.3 + - - +
344B THR* 3.7 1.2 - - - -
345B ALA* 2.8 32.1 + - - +
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Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ARG* 3.9 27.8 - - + +
19B ALA* 4.1 5.1 - - + +
23B GLN* 3.0 21.7 + - - +
340B GLY 3.5 0.4 - - - -
341B ALA* 1.3 78.1 - - - +
343B VAL* 1.3 59.6 + - + +
346B ALA* 2.9 27.7 + - - +
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ARG* 4.0 27.1 - - + +
328A TYR* 2.8 57.6 + - + +
148B ALA* 4.0 8.5 - - + -
149B GLY* 3.5 17.4 + - - +
337B ALA* 4.1 11.4 - - + +
339B ALA 4.6 6.5 - - - +
340B GLY* 3.5 6.8 + - - +
341B ALA 3.5 0.4 - - - -
342B ALA* 1.3 73.9 - - + +
344B THR* 1.3 64.0 + - - +
346B ALA* 3.5 7.7 + - - +
347B GLY 3.1 15.2 + - - -
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Residues in contact with THR 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 4.0 25.0 - - + +
115B PRO* 4.4 9.0 - - + -
144B ALA* 3.9 23.4 - - + +
148B ALA* 3.8 19.1 - - - +
149B GLY 4.4 1.1 - - - +
339B ALA* 4.1 1.7 - - - -
340B GLY 2.6 33.4 + - - -
341B ALA 3.7 2.0 - - - -
343B VAL* 1.3 73.6 - - - +
345B ALA* 1.3 59.5 + - - +
347B GLY* 2.7 22.9 + - - -
348B VAL* 3.0 11.3 + - - +
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Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 3.6 14.1 - - - +
19B ALA* 3.6 9.9 - - + -
20B PHE* 3.3 39.8 - - - +
23B GLN* 3.8 4.5 - - - +
341B ALA 2.8 17.3 + - - +
342B ALA 3.7 2.9 - - - +
344B THR* 1.3 77.2 - - - +
346B ALA* 1.3 56.6 + - - +
348B VAL* 3.2 6.9 + - - +
349B LEU* 2.9 30.3 + - - +
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Residues in contact with ALA 346 (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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158A GLU* 4.3 4.5 - - - +
159A ILE* 4.6 14.9 - - + +
162A THR* 3.7 16.5 - - + +
327A ARG* 3.3 25.1 - - - +
23B GLN* 3.3 9.1 + - - +
149B GLY* 5.1 0.2 - - - -
342B ALA 2.9 18.8 + - - +
343B VAL* 3.6 10.1 - - + +
344B THR 3.0 0.2 - - - -
345B ALA* 1.3 77.1 - - - +
347B GLY* 1.3 57.9 + - - +
350B GLY* 2.9 24.9 + - - -
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Residues in contact with GLY 347 (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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158A GLU* 4.8 6.0 - - - +
143B GLU* 4.3 7.7 - - - +
144B ALA* 4.6 5.2 - - - -
148B ALA 4.5 3.1 - - - -
149B GLY* 3.7 25.5 - - - -
343B VAL 3.1 6.7 + - - -
344B THR 2.7 14.8 + - - -
346B ALA* 1.3 70.0 - - - +
348B VAL* 1.3 62.6 + - - -
350B GLY* 3.2 3.1 + - - -
351B ASP* 3.2 24.6 + - - +
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Residues in contact with VAL 348 (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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16B VAL* 4.9 0.2 - - + -
20B PHE* 4.0 20.0 - - + -
90B VAL* 4.8 2.5 - - + -
92B ASN* 4.2 12.3 - - - +
113B ALA* 4.3 27.4 - - + +
114B THR* 4.4 2.5 - - - +
115B PRO* 3.4 32.5 - - + -
144B ALA* 3.9 11.0 - - + -
344B THR 3.0 13.4 + - - +
345B ALA* 3.6 9.0 - - - +
347B GLY* 1.3 75.1 - - - +
349B LEU* 1.3 59.9 + - - +
351B ASP* 2.9 13.1 + - - +
352B VAL* 2.9 24.8 + - + +
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Residues in contact with LEU 349 (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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162A THR* 3.9 26.0 - - + -
20B PHE* 3.8 23.0 - - + +
23B GLN* 3.7 42.4 - - + +
24B LEU* 3.9 11.2 - - + +
27B MET* 4.0 31.0 - - + -
345B ALA 2.9 17.4 + - - +
346B ALA* 4.5 0.2 - - - -
348B VAL* 1.3 76.4 - - - +
350B GLY* 1.3 57.2 + - - +
352B VAL* 3.0 16.1 + - + +
353B ILE* 2.8 36.2 + - + +
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Residues in contact with GLY 350 (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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158A GLU* 3.7 31.2 - - - +
162A THR* 4.3 0.9 - - - +
346B ALA 2.9 18.8 + - - -
347B GLY 3.2 3.6 + - - -
348B VAL 3.1 0.4 - - - -
349B LEU* 1.3 78.1 - - - +
351B ASP* 1.3 61.2 + - - +
353B ILE* 3.5 8.7 + - - +
354B LYS* 3.2 27.0 + - - +
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Residues in contact with ASP 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLU* 5.4 0.2 - - - +
113B ALA* 4.1 7.4 - - + -
114B THR 5.0 2.4 + - - +
141B TYR* 3.5 40.0 - - + +
142B HIS 3.8 0.2 - - - -
143B GLU* 2.9 47.5 + - - +
144B ALA 4.4 1.2 + - - -
347B GLY 3.2 5.5 + - - +
348B VAL* 2.9 12.3 + - - +
350B GLY* 1.3 75.4 - - - +
352B VAL* 1.3 65.0 + - - +
353B ILE 3.1 1.6 - - - -
354B LYS* 3.0 17.6 + - - +
355B ILE* 2.9 28.8 + - - +
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Residues in contact with VAL 352 (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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8B VAL* 4.8 8.7 - - + -
20B PHE* 3.9 14.4 - - + -
24B LEU* 5.6 0.9 - - + -
33B TYR* 3.7 25.8 - - + -
88B ILE* 3.7 16.6 - - + +
90B VAL* 3.6 30.1 - - + -
113B ALA* 3.8 10.7 - - + +
348B VAL 2.9 17.6 + - - +
349B LEU* 3.0 17.0 + - + +
351B ASP* 1.3 75.1 - - - +
353B ILE* 1.3 58.2 + - - +
355B ILE* 3.5 4.4 + - - -
356B ALA* 3.0 26.7 + - - +
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Residues in contact with ILE 353 (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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158A GLU* 5.0 4.3 - - + +
161A GLN* 3.6 37.9 - - + +
162A THR* 4.4 6.5 - - + -
27B MET* 3.6 32.8 - - + -
33B TYR* 3.4 22.0 - - + +
349B LEU* 2.8 27.3 + - + +
350B GLY* 3.7 7.4 - - - +
351B ASP 3.1 0.2 - - - -
352B VAL* 1.3 75.2 - - - +
354B LYS* 1.3 68.4 + - + +
356B ALA* 3.3 0.9 + - - +
357B GLN* 3.0 47.4 + - + +
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Residues in contact with LYS 354 (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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158A GLU* 2.7 30.5 + - - +
354A LYS* 6.3 2.9 - - - -
141B TYR* 3.6 35.9 - - + +
143B GLU* 5.4 2.0 + - - +
154B SER* 4.1 27.5 + - - -
350B GLY 3.2 9.6 + - - +
351B ASP* 3.0 16.4 + - - +
353B ILE* 1.3 79.3 - - + +
355B ILE* 1.3 63.5 + - - +
357B GLN* 3.3 12.0 + - - +
358B ARG* 3.1 23.9 + - - +
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Residues in contact with ILE 355 (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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88B ILE* 3.6 27.8 - - + -
111B SER* 3.8 16.6 - - - +
112B ILE 3.4 35.2 - - - +
113B ALA* 4.2 4.3 - - + -
139B PHE* 4.3 6.7 - - + -
141B TYR* 3.4 35.9 - - + -
351B ASP 2.9 17.9 + - - +
352B VAL 3.8 3.8 - - - +
354B LYS* 1.3 75.3 - - - +
356B ALA* 1.3 62.8 + - - +
358B ARG* 2.9 8.5 + - - +
359B LEU* 2.9 36.2 + - + +
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Residues in contact with ALA 356 (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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4B LYS* 2.8 28.8 + - - -
6B VAL* 4.1 20.9 - - + +
31B ILE* 3.9 8.5 - - + -
33B TYR* 3.4 34.1 - - + +
88B ILE* 4.3 5.4 - - + -
352B VAL 3.0 18.7 + - - +
353B ILE 3.3 0.9 + - - +
355B ILE* 1.3 76.5 - - - +
357B GLN* 1.3 59.0 + - - +
359B LEU* 3.3 7.3 + - - +
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Residues in contact with GLN 357 (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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141A TYR* 4.2 4.9 + - - -
161A GLN* 4.7 8.1 + - - +
354A LYS 5.5 1.0 - - - +
357A GLN 3.4 10.7 - - - +
358A ARG* 3.2 69.1 + - + +
4B LYS* 3.2 15.9 + - - +
31B ILE* 3.9 17.6 - - + +
353B ILE* 3.0 35.4 + - + +
354B LYS* 3.7 10.3 - - - +
356B ALA* 1.3 75.7 - - - +
358B ARG* 1.3 58.6 + - - +
359B LEU* 3.9 0.5 - - - +
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Residues in contact with ARG 358 (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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2A SER* 3.3 22.8 + - - +
30A THR* 5.5 5.3 + - - -
31A ILE* 5.9 4.0 - - - +
357A GLN* 3.2 58.8 + - + +
139B PHE* 3.2 49.6 - - + -
141B TYR* 2.8 38.5 + - - -
354B LYS 3.1 14.9 + - - +
355B ILE* 2.9 7.0 + - - +
357B GLN* 1.3 76.0 - - - +
359B LEU* 1.3 64.6 + - - +
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Residues in contact with LEU 359 (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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2A SER* 4.0 14.3 + - - -
358A ARG 5.6 0.2 - - - +
4B LYS* 2.8 32.5 + - - -
6B VAL* 4.5 7.4 - - + -
86B PRO* 3.5 42.7 - - + +
87B VAL 5.0 0.9 - - - +
88B ILE* 4.1 17.3 - - + -
111B SER* 4.3 8.3 - - - +
138B GLY* 6.0 1.1 - - - -
139B PHE* 3.7 23.8 - - + -
355B ILE* 2.9 35.5 + - + +
356B ALA* 3.3 7.9 + - - +
357B GLN 3.9 0.7 - - - +
358B ARG* 1.3 82.0 - - - +
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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
------------------------------------------------------------
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