Contacts of the strand formed by residues 141 - 145 (chain C) in PDB entry 1EQB
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 ASN 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B LYS* 2.8 42.8 + - - +
113C GLY* 3.7 13.9 + - - +
114C ASP 2.9 16.2 + - - +
115C THR* 3.2 27.1 + - - +
116C VAL 2.8 26.9 + - - +
140C TYR* 1.3 69.4 - - - +
142C ILE* 1.3 60.2 + - - +
143C VAL* 4.9 0.8 - - - +
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Residues in contact with ILE 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B LYS* 2.9 24.2 + - - +
193B ILE 4.1 1.4 - - - +
194B GLY* 5.2 1.0 - - - -
106C TYR* 5.3 2.5 - - + +
116C VAL* 3.5 33.7 - - + +
118C GLY 4.7 4.0 - - - +
129C HIS 4.4 7.2 - - - +
130C GLY* 3.7 42.8 - - - +
136C SER* 3.9 21.5 - - - +
137C GLY* 4.2 3.4 - - - -
140C TYR* 3.5 7.7 + - + +
141C ASN* 1.3 75.8 + - - +
143C VAL* 1.3 75.0 + - - +
144C PRO* 3.8 12.3 - - + +
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Residues in contact with VAL 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B LYS* 4.0 13.0 - - + +
192B SER 4.2 6.5 - - - +
193B ILE* 5.3 1.1 - - - -
115C THR* 3.9 23.6 - - + -
116C VAL 2.8 10.3 + - - +
117C LEU* 3.4 22.7 - - + +
118C GLY 3.1 22.9 + - - -
141C ASN* 4.9 1.1 - - - +
142C ILE* 1.3 78.5 - - - +
144C PRO* 1.3 67.3 - - + +
161C GLN* 4.0 12.6 - - - +
165C HIS* 3.7 44.4 - - + +
167C PRO* 6.2 0.4 - - + -
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Residues in contact with PRO 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ASP 3.5 23.6 - - - +
192B SER* 3.9 12.3 - - - +
193B ILE 4.1 0.4 - - - -
194B GLY* 3.9 17.0 - - - +
117C LEU* 4.7 0.4 - - - -
118C GLY 3.2 9.0 - - - +
120C ASN* 4.1 28.5 - - + +
142C ILE* 3.8 13.9 - - + +
143C VAL* 1.3 85.0 - - - +
145C TYR* 1.3 56.1 + - - +
161C GLN* 2.7 30.8 + - - -
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Residues in contact with TYR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C LEU* 3.9 14.8 - - + -
118C GLY* 3.2 20.2 + - - -
119C MET* 3.3 43.0 - - + +
120C ASN* 3.0 23.1 + - - -
144C PRO* 1.3 74.7 - - - +
146C GLY* 1.3 69.1 + - - +
153C ILE* 4.3 22.0 - - + +
158C LEU* 3.4 26.9 - - + -
161C GLN* 3.4 22.7 - - - +
170C ILE* 4.9 0.2 - - + -
171C ILE 2.6 27.2 + - - -
172C GLY* 3.8 4.9 - - - -
173C GLY 4.5 1.9 + - - -
186C MET* 3.6 17.5 - - + +
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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