Contacts of the strand formed by residues 115 - 119 (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 THR 115 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C GLY 4.7 1.0 + - - -
114C ASP* 1.3 73.5 - - - +
116C VAL* 1.3 68.0 + - - +
141C ASN* 3.2 28.7 + - - +
143C VAL* 3.9 24.5 - - + -
165C HIS* 4.3 13.8 + - + +
166C LYS 4.7 1.6 - - - -
167C PRO* 3.9 22.9 - - + -
168C LYS* 2.9 30.4 + - - +
169C MET 3.6 2.4 + - - -
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Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 4.6 5.6 - - + -
110C LEU* 3.5 30.3 - - + -
114C ASP 4.1 7.9 - - - +
115C THR* 1.3 81.8 - - - +
117C LEU* 1.3 65.3 + - - +
118C GLY 3.8 0.8 + - - +
140C TYR* 4.3 10.8 - - + -
141C ASN 2.8 6.3 + - - -
142C ILE* 3.5 20.0 - - + +
143C VAL* 2.8 28.2 + - - +
167C PRO* 4.3 2.5 - - - -
169C MET* 3.5 12.6 - - + +
171C ILE* 3.5 38.1 - - + -
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Residues in contact with LEU 117 (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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116C VAL* 1.3 74.4 - - - +
118C GLY* 1.3 53.6 + - - +
143C VAL* 3.4 34.1 - - + +
144C PRO 4.4 0.2 - - - +
145C TYR* 3.9 17.8 - - + -
158C LEU* 3.6 31.6 - - + +
161C GLN* 4.1 19.3 - - + -
162C ALA* 4.1 11.4 - - + -
165C HIS* 6.2 0.4 - - + -
167C PRO* 4.0 10.5 - - + +
169C MET 3.0 11.9 + - - +
170C ILE* 3.5 30.0 - - + +
171C ILE* 2.7 33.6 + - - +
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Residues in contact with GLY 118 (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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116C VAL* 3.8 3.0 + - - +
117C LEU* 1.3 75.8 - - - +
119C MET* 1.3 64.8 + - - -
129C HIS* 3.9 17.5 - - - -
142C ILE* 4.7 4.3 - - - +
143C VAL 3.1 6.3 + - - +
144C PRO* 3.2 8.8 - - - +
145C TYR* 3.2 26.2 + - - -
171C ILE* 4.1 14.6 - - - -
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Residues in contact with MET 119 (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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118C GLY* 1.3 70.4 - - - -
120C ASN* 1.3 70.2 + - - +
121C LEU 3.6 0.9 + - - -
123C HIS* 3.5 20.4 - - + +
124C GLY 4.1 3.8 - - - -
125C GLY* 3.3 33.9 - - - +
126C HIS 4.8 0.5 - - - +
129C HIS* 3.9 18.9 + - - +
145C TYR* 3.3 38.6 + - + +
146C GLY 4.6 2.9 - - - +
147C ILE* 3.5 24.0 - - + -
153C ILE* 4.2 19.7 - - + -
171C ILE* 4.4 1.6 + - - +
173C GLY 3.9 20.9 - - - +
174C PHE* 4.1 7.0 - - - -
177C TYR* 4.3 12.6 - - + -
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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