Contacts of the strand formed by residues 132 - 137 (chain C) in PDB entry 1EFP
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 ALA 132 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PRO* 3.5 5.5 - - - +
127C ILE* 3.0 46.4 + - + +
128C TYR* 4.9 2.5 - - + -
130C GLY 3.3 2.0 - - - -
131C ASN* 1.3 79.9 - - - +
133C ILE* 1.3 67.2 + - - +
17D ALA* 5.6 0.4 - - + -
19D VAL* 3.7 18.6 - - + -
26D VAL* 4.3 10.1 - - + -
224D VAL* 3.9 11.7 - - + -
225D ARG 3.4 5.8 - - - -
227D PRO* 4.2 1.1 - - - -
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Residues in contact with ILE 133 (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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115C SER* 4.8 8.1 - - - +
124C GLU* 3.9 30.5 - - + +
125C ARG 3.8 7.0 - - - +
126C PRO* 4.2 18.2 - - + -
130C GLY 5.4 1.6 - - - +
132C ALA* 1.3 79.7 - - - +
134C GLN* 1.3 68.5 + - - +
135C VAL* 4.0 2.2 + - + +
269C LYS* 5.4 4.3 - - - +
224D VAL* 3.1 5.4 - - - +
225D ARG* 2.8 57.2 + - + +
226D GLU 4.5 0.9 - - - -
227D PRO* 4.1 31.0 - - + -
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Residues in contact with GLN 134 (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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123C PHE 3.9 0.5 - - - +
124C GLU* 3.3 3.2 - - - -
125C ARG* 2.8 81.8 + - + +
127C ILE* 3.6 30.3 - - + +
132C ALA 4.1 1.0 - - - -
133C ILE* 1.3 74.6 - - - +
135C VAL* 1.3 60.3 + - - +
136C VAL* 3.3 23.7 + - + +
128D MET* 5.4 1.8 - - - +
219D LEU* 5.1 4.0 - - - +
221D VAL* 4.6 11.9 - - + +
223D SER 3.9 4.3 - - - +
224D VAL* 4.0 7.9 - - + -
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 3.8 28.0 - - + -
122C THR* 3.9 7.2 - - + -
123C PHE 3.4 8.7 - - - +
124C GLU* 4.2 18.8 - - + +
133C ILE 4.6 5.2 - - - +
134C GLN* 1.3 75.3 - - - +
136C VAL* 1.3 61.6 + - - +
221D VAL* 3.7 4.0 - - - +
222D VAL* 3.1 43.1 + - + +
223D SER* 3.0 27.1 + - - +
224D VAL* 5.1 0.7 - - - +
225D ARG* 4.8 9.6 - - + +
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Residues in contact with VAL 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU* 3.5 28.9 - - + -
121C ASP 3.8 0.2 - - - +
122C THR* 3.3 7.8 - - - +
123C PHE* 2.8 49.3 + - + +
125C ARG* 4.5 9.9 - - + -
134C GLN* 3.3 35.2 - - + +
135C VAL* 1.3 76.4 - - - +
137C LYS* 1.3 61.2 + - - +
138C SER 4.2 0.2 - - - -
219D LEU* 4.3 20.9 - - + -
220D GLU 3.6 8.1 - - - +
221D VAL* 4.6 7.9 - - + -
222D VAL* 5.2 1.1 - - - -
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Residues in contact with LYS 137 (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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119C ASP* 5.2 1.6 + - - -
121C ASP* 3.3 24.0 + - - +
122C THR* 3.5 26.1 + - + +
136C VAL* 1.3 76.1 - - - +
138C SER* 1.3 67.8 + - - +
139C LYS* 3.6 4.7 + - + +
219D LEU* 3.4 2.3 - - - -
220D GLU* 3.0 48.7 + - + +
222D VAL* 4.2 19.3 - - + -
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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