Contacts of the strand formed by residues 101 - 106 (chain A) in PDB entry 1ZO0
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A SER* 3.4 0.8 - - - -
98A ASP* 2.5 45.9 + - + +
99A GLU* 2.7 28.1 - - + +
100A ARG* 1.3 86.4 - - + +
102A ASN* 1.3 56.7 + - - +
103A VAL* 5.4 7.0 - - + -
118A ILE* 6.5 0.2 - - + -
119A GLN 3.7 6.3 - - - +
120A CYS* 4.3 12.1 - - + -
123A THR* 4.9 4.9 - - - +
159A LEU* 3.4 47.1 - - + -
162A PHE* 5.8 14.4 - - + -
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Residues in contact with ASN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.2 12.3 - - - +
96A TYR* 2.5 32.6 + - - +
97A SER* 3.1 18.0 + - - -
100A ARG 4.3 0.2 - - - -
101A LEU* 1.3 73.9 - - - +
103A VAL* 1.3 62.4 + - - +
104A THR* 4.0 19.8 - - - +
119A GLN* 3.0 49.9 + - + +
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Residues in contact with VAL 103 (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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95A LEU* 2.9 2.8 - - - +
96A TYR* 2.8 89.7 + - + +
98A ASP* 5.1 3.1 - - - +
101A LEU* 5.4 6.5 - - + -
102A ASN* 1.3 78.5 - - - +
104A THR* 1.3 64.7 + - - +
116A LEU* 4.5 8.3 - - + -
117A SER 3.4 5.8 - - - +
118A ILE* 3.1 33.2 - - + -
119A GLN 4.8 0.7 - - - +
166A GLN* 5.4 0.2 - - - +
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Residues in contact with THR 104 (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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94A ILE 4.4 0.7 - - - -
95A LEU* 3.0 43.3 - - + -
102A ASN* 4.0 9.0 - - - +
103A VAL* 1.3 74.5 - - - +
105A GLU* 1.3 59.9 + - - +
106A GLU* 3.0 16.8 + - - +
116A LEU* 3.2 6.5 - - - +
117A SER* 2.5 51.2 + - - +
119A GLN* 5.0 6.7 - - + +
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Residues in contact with GLU 105 (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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94A ILE* 2.7 56.7 + - + +
96A TYR* 5.2 9.9 + - + -
103A VAL 4.2 0.4 - - - -
104A THR* 1.3 71.4 - - - +
106A GLU* 1.3 65.6 + - - +
107A PRO* 3.3 25.3 - - + +
114A ARG* 5.5 11.0 + - + +
115A VAL 5.2 0.2 - - - +
116A LEU* 3.3 25.1 - - + +
134A TRP* 5.8 5.4 - - - +
167A LEU* 5.4 8.1 - - - +
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Residues in contact with GLU 106 (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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104A THR* 3.0 31.7 + - - +
105A GLU* 1.3 78.4 - - - +
107A PRO* 1.3 66.6 - - - +
108A THR* 4.6 3.3 - - - +
114A ARG* 4.3 0.8 - - - -
115A VAL* 2.9 53.5 + - + +
116A LEU* 4.1 0.5 - - - -
117A SER* 3.6 15.1 + - - -
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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