Contacts of the strand formed by residues 95 - 98 (chain A) in PDB entry 1Z16
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 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LYS 3.1 13.9 + - - +
72A TYR* 3.6 8.0 - - + -
73A VAL* 2.8 30.2 + - - +
94A ILE* 1.3 72.6 - - - +
96A MET* 1.3 59.4 + - - +
97A ILE* 4.1 16.8 - - + -
113A LEU* 3.6 20.6 - - + +
115A LEU* 3.8 22.7 - - + -
287A LEU* 3.8 22.7 - - + -
297A PRO* 3.9 21.0 - - + +
300A ILE* 3.7 28.0 - - + -
301A ALA* 4.1 18.4 - - + +
304A LEU* 5.4 0.2 - - + -
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Residues in contact with MET 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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73A VAL* 3.3 9.9 - - + -
75A GLY 3.2 23.1 - - - +
76A HIS* 4.2 3.1 - - - -
82A THR* 3.6 31.9 - - + +
86A SER* 4.2 15.0 - - - -
89A TYR* 3.6 44.2 - - + -
94A ILE 3.6 0.2 + - - -
95A LEU* 1.3 76.7 - - - +
97A ILE* 1.3 62.1 + - - +
98A THR* 4.2 7.4 - - - -
113A LEU 2.9 11.6 + - - +
114A ILE* 3.3 38.2 - - + -
115A LEU* 3.1 24.1 + - - +
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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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73A VAL 2.8 11.4 + - - +
74A ILE* 3.4 14.8 - - + +
75A GLY 2.9 21.0 + - - -
95A LEU* 4.1 25.6 - - + -
96A MET* 1.3 78.1 - - - +
98A THR* 1.3 61.2 + - - +
99A PRO* 3.5 4.2 - - - +
115A LEU* 3.3 25.8 - - + +
116A ARG 4.5 0.4 - - - -
117A THR* 4.0 17.3 - - + -
283A ALA* 3.9 35.2 - - + +
286A SER* 4.6 2.9 - - - -
287A LEU* 4.4 18.6 - - + +
304A LEU* 4.5 13.5 - - + -
318A TRP* 5.9 1.3 - - + -
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Residues in contact with THR 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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75A GLY 3.2 14.7 + - - -
76A HIS 2.7 19.6 + - - -
82A THR* 4.3 1.6 - - + -
96A MET* 4.0 14.6 - - + +
97A ILE* 1.3 72.1 - - - +
99A PRO* 1.3 62.9 - - - +
100A ALA 3.3 0.6 + - - -
101A ALA* 3.0 35.8 + - + +
106A LEU* 5.4 0.7 - - + -
114A ILE* 5.1 3.8 - - + -
115A LEU 3.0 18.8 + - - +
116A ARG* 3.2 21.0 - - + +
117A THR* 2.9 23.1 + - - -
118A THR* 4.3 0.5 + - - +
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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