Contacts of the helix formed by residues 50 - 59 (chain A) in PDB entry 1EIA
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 SER 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A THR* 1.3 70.7 - - - +
51A GLU* 1.3 65.2 + - - +
53A MET* 2.9 7.6 + - - +
54A ASN* 2.9 27.0 + - - -
107A ILE 2.7 22.2 + - - -
108A ARG 3.5 26.2 - - - -
109A GLY* 3.6 2.9 - - - -
117A GLN* 3.0 12.4 + - - -
122A PHE* 3.3 15.7 - - - -
126A ARG* 3.9 8.8 - - - +
129A TYR* 3.7 15.1 - - - -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR* 3.7 8.3 + - - +
50A SER* 1.3 76.2 - - - +
52A GLU* 1.3 67.4 + - - +
54A ASN* 2.8 23.8 + - + +
55A ALA* 2.8 13.0 + - + +
108A ARG 4.8 0.6 + - - -
109A GLY 5.5 1.6 - - - +
114A ARG* 2.9 54.9 + - - +
117A GLN* 2.9 21.4 + - - +
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR 4.1 9.7 - - - +
17A PRO* 4.5 7.2 - - + -
18A ARG* 2.9 61.0 + - - +
48A CYS* 3.7 15.4 - - + -
49A THR* 3.0 24.0 + - - +
51A GLU* 1.3 82.4 - - - +
53A MET* 1.3 58.2 + - - +
55A ALA* 3.4 15.9 - - + +
56A PHE* 2.9 24.8 - - + -
118A MET* 5.2 3.3 - - - +
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Residues in contact with MET 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.9 19.0 - - + -
45A SER* 4.2 8.1 - - - +
48A CYS* 4.0 16.6 - - + +
49A THR 3.0 21.8 + - - +
50A SER* 2.9 10.9 + - - +
52A GLU* 1.3 73.8 - - - +
54A ASN* 1.3 67.2 + - - +
55A ALA 3.0 1.6 - - - -
56A PHE* 3.0 21.9 + - + +
57A LEU* 3.2 15.1 + - - +
126A ARG 3.3 25.8 - - - +
129A TYR* 3.8 21.1 - - + -
130A ARG* 3.7 33.9 - - - +
133A ILE* 3.9 15.4 - - + +
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Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A SER 2.9 13.0 + - - +
51A GLU* 2.8 12.0 + - - +
53A MET* 1.3 77.0 - - - +
55A ALA* 1.3 57.7 + - - +
57A LEU* 2.9 17.9 + - - +
58A ASP* 2.9 37.1 + - - +
108A ARG* 3.2 22.7 - - - +
109A GLY 5.3 0.5 - - - +
110A LEU* 4.8 6.6 - - - +
129A TYR* 2.6 35.1 + - - -
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR* 4.7 8.3 - - - +
17A PRO* 3.9 22.9 - - + -
51A GLU* 2.8 13.4 + - + +
52A GLU* 3.4 16.4 - - - +
54A ASN* 1.3 77.6 - - - +
56A PHE* 1.3 60.4 + - - +
58A ASP* 3.3 9.5 + - - +
59A VAL* 3.0 31.3 + - + +
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Residues in contact with PHE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 3.8 24.0 - - + -
18A ARG* 4.2 9.0 - - + -
19A GLY* 4.2 6.1 - - - -
20A TYR 5.0 0.9 - - - -
23A TRP* 2.8 56.7 + + + +
41A PHE* 4.6 17.0 - + + -
44A LEU* 3.8 45.5 - - + -
45A SER* 4.5 4.0 - - - -
48A CYS* 4.0 20.6 - - - -
52A GLU* 2.9 28.9 - - + -
53A MET* 3.0 16.1 + - - +
55A ALA* 1.3 77.8 - - - +
57A LEU* 1.3 63.5 - - + +
59A VAL* 3.3 2.9 + - - +
60A VAL* 3.3 12.4 + - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TRP* 5.5 4.9 - - + -
41A PHE* 6.1 1.6 - - + -
53A MET 3.2 8.5 + - - +
54A ASN* 2.9 30.7 + - + +
56A PHE* 1.3 82.7 - - + +
58A ASP* 1.3 60.6 + - - +
60A VAL* 3.0 24.0 - - + +
67A LYS* 3.0 27.6 + - - -
70A LEU* 3.7 31.4 - - + -
71A LEU* 4.2 15.9 - - + -
74A ILE* 4.1 16.4 - - + -
129A TYR* 4.1 8.7 - - - +
133A ILE* 4.5 16.8 - - + -
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASN* 2.9 27.0 + - - +
55A ALA* 3.8 8.4 - - - +
56A PHE 3.2 0.4 - - - -
57A LEU* 1.3 80.5 - - - +
59A VAL* 1.3 64.6 + - + +
60A VAL 3.4 6.1 + - - +
67A LYS* 4.0 13.2 + - - +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 4.1 22.9 - - + -
20A TYR* 3.0 40.2 - - + +
23A TRP* 4.2 9.4 - - + -
24A VAL* 3.7 11.6 - - + +
55A ALA* 3.0 18.7 + - + +
56A PHE 3.3 5.1 + - - +
58A ASP* 1.3 75.1 - - + +
60A VAL* 1.3 70.9 + - - +
61A PRO* 3.0 8.0 - - - +
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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
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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