Contacts of the strand formed by residues 125 - 133 (chain C) in PDB entry 4IRQ
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C TRP* 4.5 2.2 - - + -
85C GLU 3.2 12.1 - - - +
86C GLU* 2.9 46.4 + - + +
87C ASP 3.3 20.4 + - - -
88C ALA* 4.2 8.9 + - - +
90C TRP* 2.7 42.5 + - + -
91C GLY 3.0 23.7 + - - +
92C PRO* 3.9 19.0 + - - +
93C HIS 3.9 7.7 + - - +
94C ARG* 3.5 19.4 - - + +
95C LEU* 2.8 26.7 + - - +
124C ILE* 1.3 72.9 - - - +
126C HIS* 1.3 58.8 + - - +
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Residues in contact with HIS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C HIS 4.3 0.3 - - - +
84C TRP* 3.6 6.9 - - - -
85C GLU* 3.0 48.8 + - + +
95C LEU* 3.1 17.7 - - + +
97C VAL* 4.7 1.8 - - + -
116C ARG* 3.9 21.6 + - - +
119C LEU* 3.3 43.6 - - + +
120C SER* 3.6 22.4 - - - -
124C ILE* 2.8 20.6 + - + +
125C ARG* 1.3 75.3 - - - +
127C HIS* 1.3 67.5 + - - +
128C ILE* 4.4 14.1 - - + +
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Residues in contact with HIS 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ILE* 5.9 0.7 - - + -
83C HIS* 2.9 47.8 + + - +
84C TRP* 3.8 18.8 - - + -
95C LEU 3.0 5.8 + - - +
96C ALA* 3.6 2.3 - - - -
97C VAL* 2.8 25.5 + - - +
126C HIS* 1.3 79.1 - - - +
128C ILE* 1.3 82.8 + - - +
129C TYR* 3.5 29.0 + + + -
306C PRO* 5.5 8.7 + - + +
307C CYS* 4.6 7.4 - - - -
308C THR* 2.6 33.9 + - - -
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Residues in contact with ILE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C VAL* 3.6 20.6 - - + +
99C VAL* 3.9 24.5 - - + -
111C PHE* 4.3 7.6 - - + -
112C VAL* 4.0 35.7 - - + +
115C MET* 4.0 18.2 - - + -
116C ARG* 4.5 6.3 - - + +
126C HIS* 4.4 14.8 - - + +
127C HIS* 1.3 84.6 + - - +
129C TYR* 1.3 62.1 + - - +
130C VAL* 4.5 5.6 - - + -
306C PRO 4.4 7.0 + - - +
307C CYS* 3.5 18.1 - - + +
308C THR 3.0 25.6 + - - -
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Residues in contact with TYR 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C HIS* 2.8 25.9 + + - -
84C TRP* 5.2 0.4 - + - -
96C ALA* 4.0 11.7 - - + -
97C VAL 2.7 12.6 + - - +
98C LEU* 4.1 20.0 - - + -
99C VAL* 2.8 30.8 + - - +
127C HIS* 3.5 35.2 - + + -
128C ILE* 1.3 71.8 - - - +
130C VAL* 1.3 62.8 + - - +
131C LEU* 3.5 16.7 + - + +
148C GLY 5.6 0.7 - - - -
151C GLU 4.5 4.7 - - - -
152C SER* 3.9 24.5 - - - -
153C SER* 3.1 19.4 + - - -
156C THR* 5.1 0.9 - - - -
297C ARG* 5.5 3.8 - - - -
308C THR* 3.5 24.2 - - + +
310C LEU* 4.5 13.7 - - + -
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Residues in contact with VAL 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C VAL* 3.8 7.6 - - + +
101C PHE* 3.5 42.4 - - + -
108C LEU* 3.9 25.6 - - + -
128C ILE* 4.5 8.1 - - + -
129C TYR* 1.3 73.0 - - - +
131C LEU* 1.3 56.0 + - - +
132C ASN 3.2 4.1 + - - +
307C CYS* 4.0 26.2 - - + -
308C THR 2.7 13.2 + - - +
309C VAL* 3.5 18.9 - - + +
310C LEU* 2.8 31.5 + - - +
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LEU* 3.8 28.9 - - + -
99C VAL 2.8 21.3 + - - +
100C PRO 4.5 0.2 - - - -
101C PHE* 2.8 29.5 + - - +
129C TYR* 3.8 16.4 - - + +
130C VAL* 1.3 73.4 - - - +
132C ASN* 1.3 58.0 + - - +
133C GLN 3.4 3.0 + - - -
144C LEU* 3.2 39.1 - - + +
145C ILE* 4.3 3.8 - - + -
148C GLY* 3.7 22.0 - - - -
310C LEU* 3.9 20.9 - - + -
312C ILE* 3.6 20.6 - - + -
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Residues in contact with ASN 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PHE* 3.3 35.8 - - + +
102C ARG* 4.0 6.6 - - - +
103C GLU 4.7 0.9 + - - -
130C VAL* 3.2 1.1 + - + +
131C LEU* 1.3 69.0 - - - +
133C GLN* 1.3 61.3 + - - +
134C VAL* 3.0 21.2 + - - +
309C VAL* 4.0 15.1 - - + +
310C LEU 2.7 17.5 + - - +
311C ASN* 3.1 21.8 + - - +
312C ILE* 2.9 24.3 + - - +
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Residues in contact with GLN 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PHE 2.9 13.7 + - - +
102C ARG* 3.2 46.6 + - - +
131C LEU 3.4 2.8 + - - -
132C ASN* 1.3 68.4 - - - +
134C VAL* 1.3 58.9 + - - +
135C ASP* 2.9 35.5 + - - +
137C PHE 3.9 0.4 - - - -
138C ARG 2.9 24.2 + - - -
139C PHE* 3.5 8.8 - - + -
140C ASN* 2.8 26.4 + - - +
144C LEU* 3.6 21.5 - - + +
222C TRP* 4.1 3.0 - - - -
312C ILE 3.6 4.9 - - - +
314C LEU* 3.9 15.3 - - + +
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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