Contacts of the strand formed by residues 126 - 133 (chain A) 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 HIS 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLU* 4.4 2.1 + - - +
90A TRP* 5.1 1.5 - + - -
94A ARG* 4.2 16.6 + - - +
95A LEU* 3.1 20.9 - - + +
97A VAL* 4.3 4.0 - - + -
116A ARG* 3.2 68.6 + - - +
119A LEU* 3.5 41.2 - - + +
120A SER* 3.7 18.2 - - - -
124A ILE 2.8 21.4 + - - +
125A ARG* 1.3 77.1 - - - +
127A HIS 1.3 52.4 + - - +
128A ILE* 4.2 15.9 - - + -
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Residues in contact with HIS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 5.3 0.4 - - - +
95A LEU 3.0 7.0 + - - -
96A ALA* 3.7 3.1 - - - +
97A VAL* 3.0 24.3 - - - -
126A HIS* 1.3 65.0 + - - +
128A ILE* 1.3 61.5 - - - +
129A TYR* 3.9 11.0 - - - -
156A THR* 4.9 5.3 - - - +
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Residues in contact with ILE 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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97A VAL* 3.7 19.1 - - + +
99A VAL* 4.1 22.4 - - + -
111A PHE* 4.4 7.9 - - + -
112A VAL* 4.0 29.6 - - + +
115A MET* 3.9 27.1 - - + -
116A ARG* 4.7 10.1 - - - +
126A HIS* 4.2 14.1 - - + +
127A HIS 1.3 70.8 - - - +
129A TYR* 1.3 66.4 + - - +
130A VAL* 4.5 5.2 - - + -
306A PRO 4.5 3.3 + - - +
307A CYS* 3.5 21.5 - - + +
308A THR* 3.0 26.2 + - - -
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Residues in contact with TYR 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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96A ALA* 4.0 9.0 - - + -
97A VAL 2.9 15.3 + - - +
98A LEU* 3.7 16.3 - - + -
99A VAL* 2.8 32.9 + - - +
127A HIS 3.9 20.0 - - - -
128A ILE* 1.3 74.1 - - - +
130A VAL* 1.3 60.5 + - - +
131A LEU* 3.5 17.0 + - + +
148A GLY 5.4 0.2 - - - -
151A GLU 4.5 0.2 - - - -
152A SER* 3.7 22.9 - - - -
153A SER* 2.9 36.6 + - - -
156A THR* 4.7 4.8 - - + +
297A ARG* 4.5 10.8 - - - -
308A THR* 3.3 35.4 - - + +
310A LEU* 4.0 14.6 - - + -
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Residues in contact with VAL 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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99A VAL* 3.6 6.3 - - + +
101A PHE* 3.6 41.3 - - + -
108A LEU* 3.5 31.2 - - + -
128A ILE* 4.5 5.6 - - + -
129A TYR* 1.3 72.9 - - - +
131A LEU* 1.3 57.5 + - - +
132A ASN* 3.3 4.1 + - + -
307A CYS* 3.8 26.9 - - + -
308A THR 2.8 12.2 + - - +
309A VAL* 3.5 17.3 - - + +
310A LEU* 2.8 29.8 + - - +
105B PHE* 4.8 0.7 - - + -
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Residues in contact with LEU 131 (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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98A LEU* 3.7 13.5 - - + -
99A VAL 2.8 49.8 + - - +
100A PRO* 3.5 6.5 - - + -
101A PHE* 2.8 25.7 + - - +
129A TYR* 4.1 9.4 - - + +
130A VAL* 1.3 71.3 - - - +
132A ASN* 1.3 61.0 + - - +
133A GLN 3.8 0.2 - - - -
144A LEU* 3.5 38.5 - - + +
145A ILE* 4.9 2.2 - - - +
148A GLY* 3.7 24.2 - - - +
310A LEU* 3.9 18.4 - - + -
312A ILE* 3.7 17.9 - - + -
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Residues in contact with ASN 132 (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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101A PHE* 3.7 24.4 - - + +
102A ARG* 4.8 3.5 - - - +
130A VAL* 4.3 1.6 - - + +
131A LEU* 1.3 70.7 - - - +
133A GLN* 1.3 64.4 + - - +
134A VAL* 3.3 12.8 + - - +
309A VAL* 4.0 12.1 - - + -
310A LEU 2.6 17.8 + - - +
311A ASN* 2.7 30.5 + - - +
312A ILE* 2.8 28.9 + - - +
105B PHE* 4.0 24.8 - - - -
106B GLU* 4.6 7.5 - - - +
109B LEU* 4.4 2.8 - - - +
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Residues in contact with GLN 133 (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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101A PHE 3.5 8.3 + - - -
102A ARG* 3.0 36.8 + - - +
131A LEU 3.6 2.2 + - - -
132A ASN* 1.3 72.2 + - - +
134A VAL* 1.3 58.7 + - - +
135A ASP* 3.0 35.7 + - - +
137A PHE 3.7 2.8 + - - -
138A ARG 2.9 25.2 + - - -
139A PHE* 3.4 12.1 - - + -
140A ASN* 2.9 23.0 + - - -
144A LEU* 3.8 27.7 - - + +
222A TRP* 4.1 2.2 - - - -
312A ILE 3.6 4.7 - - - +
314A LEU* 3.7 16.5 - - + +
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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