Contacts of the strand formed by residues 124 - 129 (chain C) in PDB entry 4PEI
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 LEU 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C GLN* 3.4 32.5 - - - +
9C ILE* 3.5 27.1 - - + -
39C PHE* 4.4 7.6 - - + -
119C ILE 3.7 0.3 - - - +
120C ASN* 3.2 9.9 - - - +
121C ILE 2.9 32.7 + - - +
122C ASN 3.9 0.9 - - - +
123C GLY* 1.3 83.4 - - - +
125C ARG* 1.3 61.4 + - - +
126C ILE* 4.0 11.1 - - + +
175C ASP* 3.4 29.4 - - + +
176C ILE* 4.6 6.1 - - + -
261C LEU* 4.4 15.3 - - + -
262C PRO 5.0 4.5 - - - +
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Residues in contact with ARG 125 (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 CYS* 4.0 7.2 - - - -
119C ILE 3.4 4.0 - - - -
120C ASN* 3.8 12.6 - - - +
123C GLY 5.2 2.7 - - - +
124C LEU* 1.3 74.9 - - - +
126C ILE* 1.3 60.9 + - - +
127C VAL 4.2 0.2 - - - -
168C LEU* 2.8 35.7 + - - +
171C SER* 4.3 1.3 + - - -
172C SER* 2.9 43.7 + - - +
173C GLN 3.8 5.1 + - - +
174C ILE* 3.5 24.6 - - + +
175C ASP* 2.7 39.6 + - - +
176C ILE 3.4 8.1 + - - +
272C ASP* 2.7 35.2 + - - -
274C ASP* 3.9 18.0 + - - +
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Residues in contact with ILE 126 (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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39C PHE* 4.0 31.2 - - + -
41C ILE* 4.2 4.9 - - + -
85C LEU* 4.6 4.5 - - + -
113C LEU* 4.1 7.6 - - + +
117C SER 3.8 0.5 - - - +
118C CYS* 3.0 3.6 - - - -
119C ILE* 2.8 55.1 + - + +
121C ILE* 4.0 13.5 - - + -
124C LEU* 4.3 12.6 - - + -
125C ARG* 1.3 78.5 - - - +
127C VAL* 1.3 72.0 + - - +
176C ILE* 3.3 35.9 - - + +
178C LEU* 4.0 20.9 - - + -
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Residues in contact with VAL 127 (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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113C LEU* 4.3 0.7 - - - -
117C SER 3.4 5.8 - - - +
118C CYS* 3.8 17.3 - - + -
126C ILE* 1.3 79.6 - - - +
128C GLY* 1.3 58.8 + - - +
129C VAL* 4.5 2.2 - - + -
165C LEU* 4.1 23.8 - - + -
168C LEU* 4.0 11.0 - - + -
174C ILE* 3.8 39.7 - - + +
176C ILE 2.8 7.9 + - - +
177C SER* 3.1 19.1 - - - +
178C LEU* 2.8 31.2 + - - +
217C ILE* 5.1 0.7 - - + -
221C LEU* 4.3 11.9 - - + -
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Residues in contact with GLY 128 (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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87C ILE* 3.6 19.7 - - - -
113C LEU* 3.9 10.5 - - - +
116C CYS* 3.0 29.6 - - - +
117C SER 3.1 9.6 + - - +
127C VAL* 1.3 78.3 - - - +
129C VAL* 1.3 65.3 + - - +
130C SER 4.2 0.2 - - - -
178C LEU* 3.5 6.5 - - - -
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Residues in contact with VAL 129 (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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87C ILE* 3.8 4.4 - - - +
115C VAL 4.0 3.4 - - - +
116C CYS* 4.5 0.7 - - - -
127C VAL* 4.5 6.3 - - + -
128C GLY* 1.3 74.0 - - - -
130C SER* 1.3 63.1 + - - +
131C GLY 4.0 1.0 + - - +
157C THR* 4.0 24.7 - - + -
161C VAL* 4.1 9.0 - - + -
165C LEU* 3.7 11.9 - - + -
178C LEU 2.8 16.9 + - - +
179C SER* 3.4 20.1 - - - -
180C HIS 4.0 2.1 + - - -
214C ASN* 3.4 25.4 + - - +
217C ILE* 3.6 30.5 - - + -
226C TRP* 4.5 9.6 - - + -
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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