Contacts of the helix formed by residues 88 - 99 (chain A) in PDB entry 2E31
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLU 3.2 8.7 + - - -
85A LEU* 2.9 15.7 + - - +
87A ASP* 1.3 80.9 - - - +
89A ALA* 1.3 60.7 + - - -
90A PRO* 3.6 7.2 - - - -
92A TRP* 3.1 26.9 + - - -
113A HIS* 5.5 3.2 - - - -
114A TRP* 5.4 0.2 - - - +
115A GLN 5.5 0.3 + - - -
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Residues in contact with ALA 89 (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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88A GLY* 1.3 71.7 - - - -
90A PRO* 1.4 62.7 - - + +
92A TRP* 3.1 3.6 + - - -
93A LEU* 2.7 36.5 + - + +
114A TRP* 3.8 29.9 - - + +
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Residues in contact with PRO 90 (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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56A GLU* 4.8 9.2 - - - +
60A LEU* 3.7 24.9 - - + +
85A LEU 5.4 1.3 - - - +
88A GLY* 3.6 6.5 - - - -
89A ALA* 1.4 93.6 - - + +
91A LEU* 1.3 63.3 + - - +
93A LEU* 3.7 11.9 - - + +
94A LEU* 2.8 25.8 + - - +
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Residues in contact with LEU 91 (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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60A LEU* 4.1 24.8 - - + +
63A LEU* 4.0 15.9 - - + -
64A ALA* 3.6 33.0 - - + +
71A LEU* 3.8 26.0 - - + -
85A LEU 3.7 16.8 + - - +
86A VAL* 4.0 22.0 - - + -
89A ALA 3.3 0.4 + - - -
90A PRO* 1.3 81.4 - - - +
92A TRP* 1.3 81.4 + - + +
94A LEU* 3.3 4.6 + - + +
95A LYS* 3.0 23.3 + - + +
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Residues in contact with TRP 92 (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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68A ALA* 3.5 47.6 - - + -
71A LEU* 4.1 6.5 - - + -
72A VAL* 3.8 13.0 - - + -
86A VAL* 2.7 29.0 + - + -
87A ASP 5.3 0.2 - - - -
88A GLY 3.1 24.7 - - - -
89A ALA 3.1 1.8 + - - +
91A LEU* 1.3 91.1 - - + +
93A LEU* 1.3 61.8 + - - +
94A LEU 3.1 1.3 - - - -
95A LYS* 3.0 20.0 + - + +
96A CYS* 2.8 34.4 + - - -
114A TRP* 3.6 10.5 - - + +
115A GLN* 3.2 57.5 + - + +
118A TYR* 4.1 13.7 - + + -
119A PHE* 4.0 9.2 - + - -
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Residues in contact with LEU 93 (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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89A ALA* 2.7 19.0 + - + +
90A PRO* 3.7 9.6 - - + +
92A TRP* 1.3 76.7 - - - +
94A LEU* 1.3 61.2 + - + +
96A CYS* 3.5 0.3 + - - +
97A GLN* 3.1 46.5 + - - +
102A VAL* 4.2 6.7 - - + -
109A GLU 5.5 7.9 - - - +
114A TRP* 3.9 49.8 - - + +
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Residues in contact with LEU 94 (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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57A PRO 5.1 0.2 - - - +
60A LEU* 3.6 46.2 - - + +
61A ARG* 3.9 17.5 - - + +
64A ALA* 3.8 9.2 - - + -
90A PRO 2.8 17.2 + - - +
91A LEU* 3.3 4.9 - - - +
93A LEU* 1.3 78.5 - - + +
95A LYS* 1.3 56.6 + - - +
97A GLN* 3.4 20.9 - - + +
98A GLN* 3.0 54.3 + - + +
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Residues in contact with LYS 95 (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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64A ALA* 3.0 27.4 + - - +
66A LEU 3.0 27.1 + - - -
67A PRO* 4.9 0.8 - - - +
68A ALA 4.0 6.6 - - - +
71A LEU* 3.5 25.1 - - + -
91A LEU* 3.0 17.8 + - + +
92A TRP* 3.0 32.3 + - + +
94A LEU* 1.3 75.7 - - - +
96A CYS* 1.3 61.6 + - - +
98A GLN* 3.7 7.6 - - - +
99A GLU* 3.2 43.5 + - - +
118A TYR* 3.7 26.0 + - + -
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Residues in contact with CYS 96 (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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92A TRP 2.8 18.9 + - - +
93A LEU 3.6 4.5 - - - +
95A LYS* 1.3 74.0 - - - +
97A GLN* 1.3 64.9 + - - +
99A GLU 3.2 5.7 + - - -
101A LEU* 2.9 38.4 + - + +
102A VAL* 4.1 15.5 - - + -
114A TRP* 3.9 16.4 - - + -
117A PHE* 3.5 29.8 - - + -
118A TYR* 3.9 23.3 - - - -
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Residues in contact with GLN 97 (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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93A LEU* 3.1 42.4 + - - +
94A LEU* 3.4 26.9 - - + +
96A CYS* 1.3 79.1 - - - +
98A GLN* 1.3 64.9 + - + +
100A GLY* 3.3 11.9 + - - +
102A VAL* 3.8 19.6 - - + +
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Residues in contact with GLN 98 (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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61A ARG* 4.6 14.9 + - - +
64A ALA* 3.6 40.2 + - - +
65A GLU* 4.2 15.6 + - - +
94A LEU* 3.0 38.1 + - + +
95A LYS* 3.7 8.1 - - - +
97A GLN* 1.3 80.0 - - + +
99A GLU* 1.3 66.4 + - + +
100A GLY 3.3 0.9 + - - -
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Residues in contact with GLU 99 (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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95A LYS* 3.2 24.3 + - - +
96A CYS 3.2 3.4 + - - -
98A GLN* 1.3 84.0 + - + +
100A GLY* 1.3 56.9 + - - +
101A LEU* 3.2 28.7 + - + +
118A TYR* 2.7 38.2 + - - -
122A LYS* 3.2 24.8 + - + +
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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
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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