Contacts of the strand formed by residues 116 - 121 (chain B) in PDB entry 2IZZ
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 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 6.0 0.8 - - - +
88B ASP 2.8 33.5 + - - -
89B ARG* 3.6 16.5 + - - +
90B HIS 3.5 15.9 + - - +
91B ILE* 3.6 25.6 - - + +
92B VAL* 2.8 29.4 + - - +
114B ALA 3.4 7.5 + - - +
115B PRO* 1.3 70.0 - - - +
117B VAL* 1.3 60.2 + - - +
140B HIS 3.3 26.7 - - - +
141B ALA* 4.4 1.8 - - - -
142B GLN* 3.7 26.1 + - - +
145B ASP* 2.9 43.5 + - - +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B VAL* 3.3 12.8 - - + +
94B SER 5.5 0.2 - - - +
101B ILE* 4.2 17.0 - - + -
104B ILE* 4.0 39.0 - - + -
105B GLU* 4.0 24.5 + - + +
108B LEU* 4.2 6.3 - - + -
115B PRO* 3.5 24.3 + - + +
116B ARG* 1.3 77.9 - - - +
118B ILE* 1.3 72.0 + - - +
138B GLY* 2.7 32.6 + - - -
141B ALA* 3.9 5.6 - - - +
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ILE* 4.0 13.9 - - + -
92B VAL 2.8 9.1 + - - +
93B VAL* 3.2 15.7 - - + +
94B SER* 2.8 25.6 + - - -
117B VAL* 1.3 84.5 - - - +
119B ARG* 1.3 70.3 + - - +
120B CYS* 5.1 0.4 - - + -
135B TYR* 3.9 20.6 - - + -
136B ALA 3.4 14.6 - - - +
137B THR* 4.5 7.9 - - + -
141B ALA* 4.5 5.6 - - + -
145B ASP* 3.7 23.3 - - + +
146B GLY* 4.2 6.3 - - - +
149B MET* 3.2 35.0 - - + -
153B LEU* 6.3 0.2 - - + -
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B SER* 3.5 13.5 - - - +
96B ALA 4.5 7.1 + - - +
98B GLY* 3.6 20.6 + - - +
99B VAL 3.3 26.6 + - - +
100B THR* 3.8 9.3 - - - +
101B ILE* 3.6 21.6 - - + +
104B ILE* 5.6 1.1 - - + -
118B ILE* 1.3 73.5 - - - +
120B CYS* 1.3 68.2 + - - +
121B MET* 6.3 0.2 - - - +
135B TYR* 3.1 4.0 - - - +
136B ALA 2.8 34.0 + - - +
164B GLU* 2.9 37.1 + - - +
167B ILE* 3.6 39.9 - - + +
168B ASP* 2.8 30.9 + - - -
171B THR* 5.3 0.2 + - - -
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Residues in contact with CYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 6.2 0.2 - - - -
67B PHE* 5.2 2.2 - - - -
93B VAL* 4.2 14.6 - - + -
94B SER 2.8 17.0 + - - +
95B CYS* 3.6 43.5 - - - +
96B ALA 4.6 1.6 - - - +
118B ILE 4.1 0.2 + - - -
119B ARG* 1.3 84.3 - - - +
121B MET* 1.3 69.0 + - - +
122B THR* 4.7 6.5 - - - -
133B THR* 4.4 11.7 - - + -
134B VAL 3.2 13.5 - - - +
135B TYR* 4.0 9.6 - - + +
153B LEU* 4.7 9.4 - - + -
167B ILE* 4.8 3.1 - - - +
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272A EDO 4.3 0.9 - - - +
95B CYS 3.8 14.4 - - - +
96B ALA 4.5 1.1 - - - +
97B ALA* 3.8 28.0 - - + -
98B GLY 5.3 0.2 - - - +
119B ARG* 6.3 0.2 - - - +
120B CYS* 1.3 75.2 - - - +
122B THR* 1.3 81.9 + - - +
132B ALA 3.7 1.6 - - - +
133B THR* 3.3 4.3 - - - +
134B VAL* 3.0 41.1 + - + +
167B ILE* 3.7 20.8 - - + +
170B VAL* 4.2 8.2 - - + +
171B THR* 3.5 45.8 - - + +
174B SER* 5.4 0.4 - - - +
175B GLY* 4.2 7.2 - - - -
350B NAD 3.6 16.8 - - + -
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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