Contacts of the strand formed by residues 95 - 100 (chain A) in PDB entry 4IE6
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 SER 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LEU* 3.7 31.1 + - - +
79A PHE 3.5 5.4 - - - -
80A ARG* 3.6 19.1 + - - +
93A PRO 4.0 1.3 + - - -
94A VAL* 1.3 74.9 - - - +
96A ARG* 1.3 61.2 + - - +
205A ASN* 3.1 6.2 - - - -
206A PHE* 2.8 48.0 + - - -
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Residues in contact with ARG 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A CYS 4.1 1.0 - - - +
78A LEU* 3.5 5.1 - - - -
79A PHE* 2.8 33.7 + - - +
81A ASP* 4.0 9.6 - - - +
92A THR* 3.8 19.6 + - - +
94A VAL* 3.6 31.0 - - - +
95A SER* 1.3 80.6 - - - +
97A ILE* 1.3 64.1 + - - +
108A TYR* 3.7 23.6 + - - -
113A LEU* 5.1 1.8 - - + -
203A LEU* 4.0 29.5 - - + +
204A LEU 3.0 7.4 - - - +
205A ASN* 2.5 22.8 + - - +
388A ARG* 5.2 3.8 + - - -
602A UN9 2.6 53.5 + - - -
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 4.8 6.3 - - + -
77A CYS* 3.3 27.8 - - + +
78A LEU* 3.8 12.1 - - + -
79A PHE* 5.1 4.5 - - + -
96A ARG* 1.3 76.4 - - - +
98A LEU* 1.3 71.7 + - - +
99A ILE* 3.9 10.7 + - + -
113A LEU* 5.3 0.9 - - - -
114A PHE 6.1 0.2 - - - +
116A VAL* 3.7 26.5 - - + -
203A LEU* 3.6 6.7 - - - +
204A LEU* 3.0 62.9 + - + +
388A ARG* 6.3 1.1 - - - +
389A TYR* 5.7 6.1 - - + -
392A CYS* 3.9 12.1 - - + -
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 1.3 76.1 - - - +
99A ILE* 1.3 55.7 + - - +
104A CYS 4.5 0.4 - - - +
105A THR 4.6 0.4 - - - -
106A TYR* 4.0 28.7 - - + +
113A LEU* 3.5 41.1 - - + +
114A PHE 3.8 7.8 + - - +
115A THR* 3.5 31.6 - - + +
116A VAL* 2.8 36.6 + - - +
201A VAL* 4.1 15.5 - - + -
202A THR 3.6 13.9 - - - +
203A LEU* 3.8 21.7 - - + +
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Residues in contact with ILE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.9 16.6 - - + -
97A ILE* 4.4 11.0 - - + +
98A LEU* 1.3 78.8 - - - +
100A GLY* 1.3 62.6 + - - +
115A THR* 4.1 2.7 - - - -
116A VAL* 3.2 20.0 - - + +
118A TRP* 3.5 29.7 - - + -
136A CYS* 4.2 22.7 - - + +
139A PHE* 4.0 13.2 - - + -
201A VAL* 3.5 2.3 - - - +
202A THR* 2.9 39.4 + - + +
204A LEU* 3.5 31.6 - - + -
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Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ILE* 1.3 78.5 - - - +
101A ASN* 1.3 70.8 + - - +
115A THR* 3.6 9.7 - - - +
116A VAL 3.0 7.7 + - - -
117A PRO* 3.2 5.7 - - - +
118A TRP* 3.0 41.5 + - - -
200A ASN 3.5 7.4 - - - -
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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