Contacts of the strand formed by residues 122 - 130 (chain A) in PDB entry 1ZN8
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 ARG 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A GLY 4.8 2.6 + - - -
57A ARG* 2.7 82.8 + - - +
58A ILE* 3.9 0.4 - - - -
59A ASP* 2.9 52.0 + - - +
60A TYR 3.2 6.6 + - - -
120A GLY 3.8 12.8 - - - +
121A GLN* 1.3 71.1 - - - +
123A VAL* 1.3 61.6 + - - +
149A GLU* 3.3 27.8 - - + +
151A LEU* 3.7 11.2 - - + -
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Residues in contact with VAL 123 (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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58A ILE* 4.7 0.7 - - - -
60A TYR* 3.2 16.6 - - + +
61A ILE 4.2 0.2 - - - -
62A ALA* 3.6 31.9 - - + +
84A VAL* 4.8 1.3 - - + -
117A LEU* 3.6 37.7 - - + -
121A GLN 4.2 8.3 - - - +
122A ARG* 1.3 80.3 - - - +
124A VAL* 1.3 67.6 + - - +
125A VAL 4.2 0.4 - - - -
143A LEU* 4.3 17.0 - - + -
148A ALA* 4.2 5.2 - - + -
149A GLU 2.9 8.4 + - - +
150A VAL* 3.5 6.1 - - - +
151A LEU* 2.9 28.1 + - - +
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Residues in contact with VAL 124 (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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50A LEU* 3.9 32.8 - - + -
54A HIS* 4.7 1.1 - - + -
58A ILE* 3.9 32.1 - - + -
60A TYR 3.1 5.3 + - - -
61A ILE* 3.3 20.4 - - + +
62A ALA 2.9 22.2 + - - -
75A LEU* 5.6 0.2 - - + -
123A VAL* 1.3 77.3 - - - +
125A VAL* 1.3 71.8 + - - +
126A VAL* 5.7 0.2 - - + -
151A LEU* 4.3 11.9 - - + -
152A GLU* 3.2 20.4 - - + +
154A VAL* 4.1 9.9 - - + -
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Residues in contact with VAL 125 (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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62A ALA* 3.3 10.5 - - + +
64A LEU* 3.5 40.4 - - + -
123A VAL* 4.8 0.2 - - + -
124A VAL* 1.3 77.0 - - - +
126A VAL* 1.3 64.8 + - - +
136A MET* 4.5 8.5 - - + -
139A ALA* 4.2 9.2 - - + -
140A CYS* 4.9 1.8 - - - -
143A LEU* 3.4 32.1 - - + -
150A VAL* 4.2 16.8 - - + -
152A GLU 3.2 4.4 + - - -
153A CYS* 3.3 14.7 - - - +
154A VAL* 2.9 29.6 + - - +
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Residues in contact with VAL 126 (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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46A LEU* 4.7 8.1 - - + -
61A ILE* 3.6 25.1 - - + -
62A ALA 2.9 10.9 + - - +
63A GLY* 4.2 1.8 - - - -
64A LEU* 3.2 26.4 + - - +
68A GLY* 3.8 3.5 - - - +
71A PHE* 4.2 18.4 - - + -
72A GLY* 3.7 22.4 - - - +
75A LEU* 4.3 12.3 - - + -
124A VAL 4.0 0.2 + - - -
125A VAL* 1.3 74.7 - - - +
127A ASP* 1.3 71.7 + - - +
136A MET* 4.3 2.0 - - - -
154A VAL* 3.4 25.8 - - + +
155A SER* 4.9 0.7 - - - -
156A LEU* 5.3 0.4 - - + -
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Residues in contact with ASP 127 (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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64A LEU* 3.6 28.2 - - + +
65A ASP 5.4 1.1 - - - +
66A SER 5.5 0.2 + - - -
67A ARG* 4.0 2.4 + - - +
68A GLY* 3.2 24.5 + - - -
71A PHE* 5.2 0.7 - - - -
126A VAL* 1.3 82.3 - - - +
128A ASP* 1.3 79.8 + - - +
129A LEU 3.3 5.1 - - - +
135A THR* 4.0 5.5 - - - +
136A MET* 3.4 19.4 - - + +
154A VAL 3.3 4.9 + - - +
155A SER* 3.1 19.6 - - - -
156A LEU* 3.8 1.8 + - - +
1031A AMP 3.1 30.6 + - - -
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Residues in contact with ASP 128 (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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27A ARG 4.9 1.9 - - - +
29A ILE* 3.7 30.9 - - + +
67A ARG* 2.6 47.9 + - + +
68A GLY* 4.4 3.2 - - - +
71A PHE* 4.1 12.6 - - + -
127A ASP* 1.3 81.9 + - - +
129A LEU* 1.3 68.6 + - - +
156A LEU* 2.9 33.4 + - - +
157A VAL* 3.1 8.3 + - - +
1031A AMP 2.7 21.0 + - - -
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Residues in contact with LEU 129 (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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27A ARG* 3.9 20.9 - - + +
29A ILE* 6.2 1.1 - - + -
127A ASP* 3.3 8.4 - - - +
128A ASP* 1.3 95.1 + - - +
130A LEU* 1.3 77.4 + - - +
131A ALA* 3.6 16.2 - - + +
136A MET* 5.0 1.8 - - - +
155A SER* 4.0 4.5 - - - -
157A VAL* 3.2 37.9 - - + +
159A LEU* 3.8 14.6 - - + -
1031A AMP 3.6 52.3 - - + +
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Residues in contact with LEU 130 (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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129A LEU* 1.3 77.5 - - - +
131A ALA* 1.3 64.7 + - - +
133A GLY* 3.6 26.2 - - - -
136A MET* 3.4 28.5 - - + -
155A SER* 3.7 1.2 + - - +
157A VAL 2.8 10.5 + - - +
158A GLU* 4.3 9.4 - - + -
159A LEU 3.0 24.8 + - - -
164A GLY* 3.6 4.7 - - - +
165A ARG 3.5 27.4 - - - +
168A LEU* 3.9 9.4 - - + -
173A PHE* 3.6 43.3 - - + -
1031A AMP 4.3 1.8 - - - +
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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