Contacts of the strand formed by residues 130 - 134 (chain B) in PDB entry 1EGE
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 MET 130 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B TYR* 3.0 32.1 - - + +
53B ILE* 3.6 34.8 - - + -
62B MET* 3.5 28.0 - - + -
97B ALA 3.1 25.4 - - - +
98B ILE* 4.7 0.7 - - - -
101B ASN* 3.2 5.8 - - - +
124B MET* 4.2 0.8 - - - +
128B PRO 4.8 2.9 - - - +
129B LEU* 1.3 76.3 - - - +
131B CYS* 1.3 58.9 + - - +
169B ASN* 3.5 15.9 - - - +
172B LYS 3.5 21.9 + - - +
173B ALA* 3.9 1.1 - - - -
174B ASN* 2.7 34.9 + - - +
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Residues in contact with CYS 131 (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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100B GLY 3.6 11.6 - - - +
101B ASN* 2.8 38.7 + - - +
104B GLY 4.2 3.8 - - - -
105B GLN* 4.0 2.7 - - - -
124B MET* 3.5 24.5 - - + -
130B MET* 1.3 76.6 - - - +
132B ALA* 1.3 57.9 + - - +
169B ASN* 3.9 7.9 + - - +
173B ALA* 3.5 5.6 - - - -
175B TRP* 3.1 53.4 - - + +
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Residues in contact with ALA 132 (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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100B GLY 4.8 2.2 - - - -
104B GLY* 3.4 14.7 - - - -
131B CYS* 1.3 74.1 - - - +
133B TYR* 1.3 61.2 + - - +
134B CYS 3.9 0.9 - - - -
167B ILE* 3.6 11.4 - - + -
168B THR 3.3 23.1 - - - +
169B ASN* 4.2 3.4 - - - -
173B ALA* 3.5 5.0 - - + +
175B TRP* 3.2 8.8 + - - +
176B TYR* 3.4 27.3 - - + -
177B PHE 3.1 21.7 + - - -
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Residues in contact with TYR 133 (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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100B GLY 5.1 1.7 + - - +
103B LEU* 3.5 41.1 - - + -
104B GLY* 4.2 8.7 - - - +
107B PRO* 4.1 10.1 - - + -
132B ALA* 1.3 74.6 - - - +
134B CYS* 1.3 60.1 + - - +
135B VAL* 3.3 26.0 - - + +
167B ILE* 3.7 3.8 - - - +
168B THR 4.7 1.4 + - - -
177B PHE* 3.5 27.6 - + - +
248B ALA* 3.8 18.0 + - - +
251B ALA* 5.0 5.4 - - + -
252B PHE* 3.2 37.6 - + - -
399B FAD 2.9 46.1 + + - +
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Residues in contact with CYS 134 (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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133B TYR* 1.3 70.1 - - - +
135B VAL* 1.3 64.9 + - - +
164B LYS* 3.6 19.2 + - + -
167B ILE* 3.6 31.0 - - - -
176B TYR* 3.7 31.6 - - - -
177B PHE 2.7 15.2 + - - +
178B LEU* 3.2 31.2 - - + -
179B LEU 3.2 2.9 + - - -
225B ILE* 4.5 4.9 - - - -
227B PHE* 4.3 13.9 - - - -
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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