Contacts of the strand formed by residues 150 - 158 (chain A) in PDB entry 5ZF6
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 THR 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A VAL 3.2 12.6 - - - +
86A SER* 3.1 19.9 + - - -
96A MET* 5.2 2.0 - - - +
97A PRO 2.8 18.2 + - - +
98A LEU* 3.5 25.4 - - + +
99A VAL* 3.3 18.7 + - - +
142A PHE* 4.3 15.9 - - + -
146A TYR* 3.7 10.0 - - - -
148A TYR 2.9 14.4 + - - -
149A ASP* 1.3 72.3 + - - +
151A GLN* 1.3 70.1 + - - +
152A VAL* 4.8 1.1 - - + -
177A LEU* 4.8 4.3 - - + -
182A ILE* 4.6 7.6 - - + -
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Residues in contact with GLN 151 (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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83A THR 3.6 0.7 - - - +
84A ALA* 3.2 5.0 - - - +
85A VAL* 2.8 55.1 + - + +
87A LYS* 4.7 7.4 + - - -
99A VAL* 3.7 20.5 - - + +
149A ASP* 3.9 17.0 - - - +
150A THR* 1.3 78.1 - - - +
152A VAL* 1.3 63.9 + - - +
153A LEU* 4.0 4.4 - - + +
103B ARG* 5.6 6.1 - - - +
155B ASN* 4.4 11.5 + - - +
156B LEU 4.2 16.8 + - - +
157B LEU* 4.5 15.5 - - - +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 3.6 26.9 - - + -
83A THR 3.2 3.4 - - - +
84A ALA* 4.3 13.5 - - + -
98A LEU* 4.6 10.3 - - + -
99A VAL 3.1 7.1 + - - -
100A VAL* 3.3 20.8 - - + +
101A ASP* 2.9 26.6 + - - +
138A ILE* 4.0 19.7 - - + -
150A THR* 4.8 1.1 - - + -
151A GLN* 1.3 77.5 - - - +
153A LEU* 1.3 57.5 + - - +
154A CYS* 3.9 5.5 + - - -
173A ALA* 3.8 18.2 - - + -
177A LEU* 4.6 11.7 - - + -
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Residues in contact with LEU 153 (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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81A MET 3.7 1.2 - - - +
82A VAL* 3.1 2.5 - - - -
83A THR* 2.7 55.7 + - - +
101A ASP* 3.6 8.5 - - + +
103A ARG* 3.1 36.8 - - - +
151A GLN* 4.0 4.6 - - + +
152A VAL* 1.3 70.8 - - - +
154A CYS* 1.3 72.3 + - - +
155A ASN* 5.0 7.8 - - + +
81B MET* 5.9 1.8 - - + -
153B LEU* 4.5 16.2 - - + -
155B ASN* 4.0 32.1 - - + +
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Residues in contact with CYS 154 (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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80A VAL* 4.4 1.8 - - + -
81A MET 3.5 4.5 - - - -
82A VAL* 3.8 29.6 - - + -
100A VAL* 4.4 10.3 - - - -
101A ASP 2.7 20.8 + - - +
102A TYR* 3.8 19.7 - - + -
103A ARG* 3.2 27.6 + - - +
134A ILE* 3.8 28.7 - - - -
152A VAL* 4.4 4.3 - - - -
153A LEU* 1.3 75.3 - - - +
155A ASN* 1.3 60.2 + - - +
156A LEU* 5.4 0.2 - - - -
169A ALA* 4.1 6.1 - - + -
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Residues in contact with ASN 155 (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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80A VAL* 3.6 1.0 - - - +
81A MET* 2.6 49.8 + - + +
103A ARG* 3.9 7.6 - - - +
153A LEU* 5.0 9.6 - - + +
154A CYS* 1.3 74.8 - - - +
156A LEU* 1.3 76.3 + - - +
157A LEU* 3.4 24.1 + - - +
153B LEU* 3.5 31.4 - - + +
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Residues in contact with LEU 156 (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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79A ALA 4.1 3.8 - - - +
80A VAL* 3.8 22.2 - - + +
102A TYR* 3.7 25.8 - - + +
103A ARG* 3.3 36.2 - - + +
104A GLN* 4.1 18.4 - - + +
155A ASN* 1.3 81.9 + - - +
157A LEU* 1.3 63.4 + - - +
158A ALA 5.2 0.4 - - - +
159A VAL* 3.8 22.7 - - + -
165A PRO* 3.7 26.0 - - + -
151B GLN* 4.8 6.6 + - - -
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Residues in contact with LEU 157 (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 VAL* 4.6 12.3 - - + -
79A ALA* 3.0 24.8 + - + +
81A MET* 4.1 28.7 - - + +
155A ASN* 3.4 28.9 - - - +
156A LEU* 1.3 74.6 - - - +
158A ALA* 1.3 63.1 + - + +
85B VAL* 6.3 3.1 - - + -
87B LYS* 3.8 18.5 + - - -
151B GLN* 3.9 13.1 + - - +
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Residues in contact with ALA 158 (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 ASP 3.5 18.4 - - - +
78A THR* 3.3 7.2 - - - +
79A ALA* 3.2 29.0 + - + +
156A LEU* 3.6 1.4 - - - +
157A LEU* 1.3 82.5 + - + +
159A VAL* 1.3 68.9 + - - +
87B LYS* 5.5 7.2 - - - +
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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