Contacts of the helix formed by residues 14 - 27 (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 14 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B GLY* 3.6 2.8 + - - -
13B ALA* 1.3 75.9 - - - +
15B VAL* 1.3 60.8 + - - -
16B VAL 3.3 2.2 - - - -
17B GLY 4.1 3.0 - - - +
18B SER* 2.8 33.5 + - - +
40B GLU* 4.0 3.9 + - - -
92B ASN 5.5 2.2 + - - -
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Residues in contact with VAL 15 (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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14B GLY* 1.3 73.3 - - - +
16B VAL* 1.3 67.2 + - + +
18B SER* 4.1 2.4 - - - -
19B ALA* 3.6 8.8 + - - +
341B ALA* 3.4 35.4 - - + +
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY* 4.5 0.2 - - - -
15B VAL* 1.3 79.7 - - + +
17B GLY* 1.3 62.1 + - - +
18B SER 3.1 1.3 - - - -
19B ALA* 2.9 6.2 + - - +
20B PHE* 2.8 25.2 + - + +
92B ASN* 4.3 20.9 - - - +
115B PRO* 4.4 11.2 - - + -
340B GLY 5.4 0.2 - - - -
341B ALA* 4.5 13.2 - - - +
344B THR* 4.0 35.7 - - + +
345B ALA* 3.6 15.6 - - - +
348B VAL* 4.9 0.2 - - + -
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY 3.5 12.3 - - - -
13B ALA* 4.1 7.2 - - - -
14B GLY 3.8 4.8 + - - +
16B VAL* 1.3 79.8 - - - +
18B SER* 1.3 52.1 + - - +
20B PHE* 3.1 3.0 + - - +
21B LEU* 2.8 39.4 + - - +
92B ASN* 3.3 33.0 + - - +
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Residues in contact with SER 18 (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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13B ALA 3.9 6.0 - - - -
14B GLY 2.8 23.8 + - - -
15B VAL* 4.1 3.4 - - - -
17B GLY* 1.3 76.0 - - - +
19B ALA* 1.3 61.7 + - - +
21B LEU 3.5 0.2 + - - -
22B ASP* 3.2 28.4 + - - +
59B TRP* 3.4 19.3 - - - -
60B LYS* 2.8 32.9 + - - -
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Residues in contact with ALA 19 (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 3.6 7.8 + - - +
16B VAL 2.9 8.1 + - - +
18B SER* 1.3 76.3 - - - +
20B PHE* 1.3 65.9 + - - +
22B ASP* 3.4 7.6 + - - +
23B GLN* 3.0 31.0 + - - +
341B ALA* 3.9 22.2 - - + +
342B ALA* 4.1 8.1 - - + +
345B ALA* 3.6 14.8 - - + -
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Residues in contact with PHE 20 (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* 4.7 1.6 - - + -
10B VAL* 3.7 14.1 - - + -
16B VAL 2.8 12.8 + - - +
17B GLY 3.2 9.0 - - - +
19B ALA* 1.3 77.9 - - - +
21B LEU* 1.3 56.1 + - + +
23B GLN* 3.3 5.0 + - - +
24B LEU* 2.8 57.3 + - + +
90B VAL* 3.6 35.4 - - + -
92B ASN* 3.6 23.6 - - - +
345B ALA* 3.3 27.5 - - + +
348B VAL* 4.0 9.9 - - + -
349B LEU* 3.8 34.3 - - + -
352B VAL* 3.9 11.4 - - + -
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Residues in contact with LEU 21 (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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10B VAL* 3.9 31.2 - - + -
12B GLY 5.0 0.4 - - - +
13B ALA* 3.9 7.6 - - + -
17B GLY 2.8 22.3 + - - +
18B SER 3.8 0.9 - - - +
20B PHE* 1.3 78.5 - - + +
22B ASP* 1.3 63.6 + - - +
24B LEU* 3.3 4.1 + - + +
25B LEU* 3.0 31.0 + - + +
35B LEU* 4.0 25.1 - - + -
38B LEU* 3.8 22.7 - - + -
59B TRP* 3.6 51.8 - - + +
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Residues in contact with ASP 22 (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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18B SER* 3.2 16.2 + - - +
19B ALA* 3.7 10.4 - - - +
21B LEU* 1.3 77.9 - - - +
23B GLN* 1.3 66.3 + - + +
25B LEU* 3.3 3.8 + - - +
26B ALA* 3.1 25.7 + - - +
59B TRP* 2.6 36.0 + - - +
60B LYS* 4.9 3.9 + - - -
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Residues in contact with GLN 23 (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* 3.6 21.4 - - - +
327A ARG* 3.3 28.7 - - - +
19B ALA* 3.0 20.1 + - - +
20B PHE* 3.6 4.0 - - - +
22B ASP* 1.3 78.1 - - + +
24B LEU* 1.3 64.1 + - - +
26B ALA* 3.3 4.8 + - - +
27B MET* 3.0 26.2 + - - +
342B ALA* 3.0 35.6 + - - +
345B ALA* 3.8 9.3 - - - +
346B ALA* 3.3 25.8 + - - -
349B LEU* 3.7 10.1 - - + +
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Residues in contact with LEU 24 (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* 4.3 19.5 - - + -
20B PHE* 2.8 42.0 + - + +
21B LEU* 3.5 7.6 - - + +
22B ASP 3.2 0.2 - - - -
23B GLN* 1.3 76.0 - - - +
25B LEU* 1.3 65.2 + - + +
26B ALA 3.2 1.0 + - - -
27B MET* 3.5 16.4 + - + +
33B TYR* 3.8 35.4 - - + +
35B LEU* 4.0 36.1 - - + +
349B LEU* 3.9 19.5 - - + +
352B VAL* 5.6 0.9 - - + -
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Residues in contact with LEU 25 (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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21B LEU* 3.0 17.9 + - + +
22B ASP* 4.1 4.0 - - - +
24B LEU* 1.3 80.5 - - + +
26B ALA* 1.3 58.9 + - - +
27B MET 4.8 2.1 - - - +
33B TYR 6.1 0.7 - - - +
35B LEU* 4.1 32.5 - - + +
55B VAL* 4.1 25.1 - - + -
57B SER 5.6 3.4 - - - +
59B TRP* 3.7 32.3 - - + -
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Residues in contact with ALA 26 (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 6.0 0.7 - - - +
22B ASP 3.1 17.2 + - - +
23B GLN* 3.8 4.9 - - - +
24B LEU 3.1 0.2 - - - -
25B LEU* 1.3 80.0 - - - +
27B MET* 1.3 65.9 + - - +
28B LYS* 3.6 19.8 + - - +
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Residues in contact with MET 27 (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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161A GLN* 3.3 29.4 - - + +
162A THR* 5.1 2.2 + - - -
163A GLY* 6.5 0.2 - - - -
23B GLN 3.0 16.7 + - - +
24B LEU* 3.5 14.2 + - + +
25B LEU 4.8 1.6 - - - +
26B ALA* 1.3 78.6 - - - +
28B LYS* 1.3 70.7 + - - +
29B SER* 4.2 6.5 + - - -
33B TYR* 3.5 44.6 - - + -
349B LEU* 4.0 28.0 - - + -
353B ILE* 3.6 26.9 - - + -
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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
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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