Contacts of the helix formed by residues 85 - 93 (chain A) in PDB entry 3ELW
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A VAL* 3.6 5.6 - - - -
82A CYS 2.9 16.2 + - - -
83A GLY 4.2 0.2 - - - -
84A ARG* 1.3 79.4 - - - +
86A GLY* 1.3 60.1 + - - +
87A TRP 3.3 2.7 - - - -
88A SER* 3.0 6.3 + - - -
89A TYR* 3.0 34.8 + - - -
126A PHE* 4.1 21.8 - - - -
4633A SAM 3.7 0.4 + - - -
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Residues in contact with GLY 86 (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 SER* 5.3 0.9 + - - -
55A VAL* 3.4 14.4 - - - +
56A SER* 3.4 21.8 - - - -
59A ALA* 3.6 16.7 - - - +
85A GLY* 1.3 76.2 - - - +
87A TRP* 1.3 62.4 + - - +
89A TYR* 4.3 2.3 - - - +
90A TYR* 3.3 22.2 + - - +
4633A SAM 3.1 10.4 + - - -
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Residues in contact with TRP 87 (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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58A GLY 2.8 26.3 + - - -
61A LYS* 4.3 9.8 - - + +
62A ILE* 3.6 40.4 - - + +
65A LEU* 5.0 1.3 - - + -
79A ASP* 3.5 18.8 - - - +
85A GLY 3.3 0.6 - - - -
86A GLY* 1.3 73.2 - - - +
88A SER* 1.3 60.7 + - - +
90A TYR* 3.5 1.6 + - - +
91A ALA* 3.0 29.5 + - - +
144A LEU* 3.8 31.6 - - + +
145A CYS 4.2 2.5 - - - -
146A ASP* 3.4 34.3 + - + -
180A CYS* 3.8 28.5 - - + -
220A TYR* 3.5 31.6 - + - -
4633A SAM 3.2 32.2 + - - +
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Residues in contact with SER 88 (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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79A ASP* 2.7 32.6 + - - +
82A CYS* 3.9 1.6 - - - +
85A GLY 3.0 9.3 + - - -
87A TRP* 1.3 78.9 - - - +
89A TYR* 1.3 58.0 + - - +
91A ALA* 3.5 3.9 + - - +
92A ALA* 3.0 28.1 + - - +
100A VAL* 3.8 23.6 - - - +
102A GLY* 4.0 2.8 - - - -
124A VAL* 4.5 3.8 - - - -
126A PHE* 3.6 29.6 - - - -
144A LEU* 5.9 0.2 - - - -
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Residues in contact with TYR 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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53A ILE 6.1 0.4 - - - +
54A SER* 6.3 2.2 - - - -
55A VAL* 4.2 16.8 - - + +
84A ARG 4.5 1.8 - - - -
85A GLY 3.0 26.5 + - - +
86A GLY* 4.5 2.9 - - - +
88A SER* 1.3 73.6 - - - +
90A TYR* 1.3 67.7 + - - +
92A ALA* 3.4 4.8 + - + +
93A ALA* 3.3 21.0 + - - +
114A ILE 3.0 22.9 + - - -
116A MET* 3.0 43.5 + - + -
118A THR* 3.5 23.9 + - - +
119A LEU 4.4 2.5 - - - +
121A TRP* 4.2 9.9 - - + -
124A VAL* 4.4 11.0 - - + -
126A PHE* 3.4 22.3 - + - -
259A LEU* 3.8 9.8 - - + +
295A SO4 3.2 27.9 + - - -
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Residues in contact with TYR 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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54A SER* 6.0 0.2 - - - +
59A ALA* 4.8 2.9 - - + -
62A ILE* 3.6 22.7 - - + -
63A ARG* 3.7 40.0 + - + +
66A HIS* 2.8 40.7 - + + +
67A GLU* 4.3 5.6 + - - +
73A ILE* 3.7 17.9 - - + -
86A GLY 3.3 20.0 + - - +
87A TRP 3.7 4.5 - - - +
89A TYR* 1.3 79.8 - - - +
91A ALA* 1.3 63.8 + - - +
93A ALA* 3.3 4.7 + - - +
94A GLN* 2.9 46.0 + - - +
257A VAL* 3.9 22.4 - - + -
259A LEU* 4.4 14.0 - - + +
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Residues in contact with ALA 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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73A ILE* 3.9 23.1 - - + -
77A VAL* 4.1 14.6 - - + -
87A TRP 3.0 18.1 + - - +
88A SER* 3.7 5.6 - - - +
90A TYR* 1.3 80.5 - - + +
92A ALA* 1.3 61.5 + - - +
94A GLN* 3.0 19.5 + - - +
97A VAL* 3.2 19.9 - - - +
100A VAL* 4.1 11.4 - - + -
144A LEU* 4.6 4.0 - - + -
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Residues in contact with ALA 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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88A SER 3.0 10.6 + - - +
89A TYR* 3.8 7.9 - - + +
90A TYR 3.3 0.4 - - - -
91A ALA* 1.3 76.8 - - - +
93A ALA* 1.3 52.9 + - - +
97A VAL* 4.3 3.6 - - - -
100A VAL* 3.7 11.4 - - + +
119A LEU 3.5 5.9 - - - +
120A GLY* 3.5 14.2 - - - +
121A TRP* 5.2 0.2 - - - -
123A ILE* 3.8 4.1 - - + +
124A VAL* 3.4 33.2 - - + -
264A ARG* 2.7 35.4 + - - -
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Residues in contact with ALA 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 TYR 3.3 7.3 + - - +
90A TYR 3.3 9.8 + - - +
91A ALA 3.1 1.2 + - - -
92A ALA* 1.3 76.1 - - - +
94A GLN* 1.3 67.4 + - - +
95A LYS* 3.9 1.9 + - - +
119A LEU* 3.4 45.0 + - + +
259A LEU* 4.0 25.1 - - + -
260A PRO* 4.9 3.1 - - + +
264A ARG* 4.2 2.8 + - - -
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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