Contacts of the strand formed by residues 125 - 133 (chain B) in PDB entry 4IRP
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 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLU* 3.0 43.4 + - - +
87B ASP 2.9 28.9 + - - -
88B ALA* 4.0 7.3 + - - +
90B TRP* 3.4 23.4 - - + +
91B GLY 2.4 38.4 + - - +
92B PRO* 4.9 2.2 - - - -
93B HIS 3.6 20.1 + - - +
94B ARG* 3.5 32.8 - - + +
95B LEU* 2.8 24.4 + - - +
123B LYS 3.7 0.8 + - - -
124B ILE* 1.3 73.3 - - - +
126B HIS* 1.3 61.7 + - - +
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Residues in contact with HIS 126 (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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86B GLU* 4.3 1.7 + - - +
90B TRP* 5.1 1.5 - + - -
94B ARG* 4.1 15.2 + - - +
95B LEU* 3.2 22.4 - - + +
97B VAL* 4.4 3.1 - - + -
115B MET 4.0 2.0 + - - -
116B ARG* 3.3 72.6 + - - +
119B LEU* 3.5 37.1 - - + +
120B SER* 3.9 13.9 - - - -
124B ILE 2.8 20.6 + - - +
125B ARG* 1.3 76.8 - - - +
127B HIS* 1.3 63.1 + - - +
128B ILE* 4.0 17.0 - - + +
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Residues in contact with HIS 127 (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 ARG* 5.4 3.4 - - - -
95B LEU 3.0 6.6 + - - +
96B ALA* 3.6 1.2 - - - -
97B VAL* 2.8 25.8 + - - +
116B ARG* 4.7 2.9 - - - +
126B HIS* 1.3 77.2 + - - +
128B ILE* 1.3 90.0 + - - +
129B TYR* 3.2 41.9 + + + +
153B SER* 5.9 1.2 - - - -
156B THR* 4.6 7.6 - - + -
306B PRO* 6.5 1.3 - - + -
307B CYS* 4.6 2.4 - - - -
308B THR* 2.6 32.8 + - - -
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Residues in contact with ILE 128 (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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97B VAL* 3.7 15.7 - - + +
99B VAL* 4.2 21.1 - - + -
111B PHE* 4.4 8.3 - - + -
112B VAL* 4.0 31.4 - - + +
115B MET* 3.9 27.4 - - + -
116B ARG* 4.6 6.6 - - + +
126B HIS* 4.0 16.4 - - + +
127B HIS* 1.3 83.9 - - - +
129B TYR* 1.3 64.4 + - - +
130B VAL* 4.5 5.6 - - + -
306B PRO 4.4 4.5 - - - +
307B CYS* 3.4 20.2 - - + +
308B THR 3.0 24.1 + - - -
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Residues in contact with TYR 129 (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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96B ALA* 3.9 25.1 - - + -
97B VAL 2.8 14.4 + - - +
98B LEU* 3.8 9.1 - - + -
99B VAL* 2.7 33.1 + - - +
127B HIS* 3.2 51.2 + + + +
128B ILE* 1.3 72.1 - - - +
130B VAL* 1.3 60.6 + - - +
131B LEU* 3.6 18.4 + - + +
148B GLY 5.4 0.4 - - - -
151B GLU 4.4 4.9 - - - -
152B SER* 3.7 14.8 - - - -
153B SER* 2.9 36.6 + - - -
156B THR* 4.7 1.0 - - + +
308B THR* 3.5 18.8 - - + +
310B LEU* 4.2 18.8 - - + -
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Residues in contact with VAL 130 (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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105A PHE* 4.7 0.4 - - + -
99B VAL* 3.6 6.7 - - + +
101B PHE* 3.6 40.4 - - + -
108B LEU* 3.9 24.5 - - + -
128B ILE* 4.5 6.1 - - + -
129B TYR* 1.3 72.0 - - - +
131B LEU* 1.3 62.9 + - - +
132B ASN* 3.3 2.8 + - + -
307B CYS* 3.8 32.5 - - + -
308B THR 2.8 11.8 + - - +
309B VAL* 3.5 17.5 - - + -
310B LEU* 2.8 31.0 + - - +
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Residues in contact with LEU 131 (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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98B LEU* 3.7 18.4 - - + -
99B VAL 2.7 42.4 + - - +
100B PRO* 3.9 8.0 - - + +
101B PHE* 3.0 23.8 + - - +
129B TYR* 4.0 10.8 - - + -
130B VAL* 1.3 75.0 - - - +
132B ASN* 1.3 60.3 + - - +
133B GLN 3.4 1.8 + - - -
144B LEU* 3.9 33.4 - - + +
145B ILE* 4.6 2.5 - - - -
148B GLY* 3.7 22.9 - - - +
310B LEU* 3.8 24.7 - - + -
312B ILE* 4.1 13.7 - - + -
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Residues in contact with ASN 132 (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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105A PHE* 4.0 25.4 - - - -
106A GLU* 4.8 6.9 - - - +
109A LEU* 4.4 2.4 - - - +
101B PHE* 3.7 23.5 - - + +
102B ARG* 4.6 3.6 - - - -
103B GLU 5.2 0.7 + - - -
130B VAL 4.3 0.9 - - - +
131B LEU* 1.3 70.1 - - - +
133B GLN* 1.3 61.1 + - - +
134B VAL* 3.1 20.9 + - - +
309B VAL* 3.9 11.4 - - + -
310B LEU 2.7 19.1 + - - +
311B ASN* 2.5 26.9 + - - +
312B ILE* 2.9 27.4 + - - +
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Residues in contact with GLN 133 (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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101B PHE 3.3 9.9 + - - -
102B ARG* 3.2 37.7 + - - +
131B LEU 3.4 1.8 + - - -
132B ASN* 1.3 72.5 + - - +
134B VAL* 1.3 57.2 + - - +
135B ASP* 3.0 38.6 + - - +
138B ARG 2.9 24.6 + - - -
139B PHE* 3.4 12.1 - - + -
140B ASN* 2.7 24.6 + - - +
144B LEU* 3.3 32.4 - - + +
222B TRP* 4.1 3.2 - - - -
312B ILE 3.7 4.5 - - - +
314B LEU* 3.7 14.7 - - + +
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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