Contacts of the strand formed by residues 145 - 153 (chain C) in PDB entry 1I3R
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 PHE 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.9 14.8 - + - -
111C LYS 3.2 14.2 + - - -
112C PHE* 3.0 52.0 + - + +
113C SER* 3.6 12.6 - - - -
115C PRO* 3.5 40.4 - - + -
137C PHE* 4.0 15.5 - - + -
138C LEU 3.6 12.8 - - - +
140C ARG* 3.8 2.9 - - - -
143C HIS 4.0 8.3 - - - -
144C LEU* 1.3 75.6 - - - +
146C ARG* 1.3 60.7 + - - +
34D LEU* 3.8 11.9 - - + -
36D TYR* 3.4 52.0 - + - -
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Residues in contact with ARG 146 (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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25C ASP* 4.6 2.8 + - - -
28C GLY* 2.9 33.9 + - - -
108C PHE* 3.9 21.5 - - + -
109C ILE 3.2 9.9 - - - +
110C ASP* 3.4 18.8 - - - +
112C PHE* 3.7 2.9 - - - -
137C PHE* 3.7 2.1 - - - -
138C LEU* 2.9 54.9 + - + +
139C PRO 3.4 19.8 + - - -
140C ARG* 4.0 16.3 - - + +
145C PHE* 1.3 73.1 - - - +
147C LYS* 1.3 62.7 + - - +
148C PHE* 3.2 33.5 - - - -
175D ARG* 3.9 16.7 - - - +
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Residues in contact with LYS 147 (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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107C CYS 3.7 0.7 - - - +
108C PHE* 3.8 3.8 - - - -
109C ILE* 2.7 43.6 + - + +
112C PHE* 4.1 12.3 - - + -
117C VAL* 4.0 24.8 + - + +
134C GLU* 2.8 23.7 + - - -
135C THR* 3.0 34.1 - - - +
136C VAL* 3.8 8.3 - - - +
137C PHE* 4.1 26.0 - - + -
138C LEU* 5.0 0.4 - - - -
146C ARG* 1.3 77.9 - - - +
148C PHE* 1.3 69.7 + - - +
149C HIS* 3.2 29.1 + - + +
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Residues in contact with PHE 148 (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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106C ILE* 3.9 17.7 - - + -
107C CYS 3.7 1.8 - - - -
108C PHE* 3.5 36.3 - + + -
134C GLU* 3.4 2.9 - - - -
135C THR* 3.0 38.3 + - + +
138C LEU* 3.7 17.9 - - + -
146C ARG* 3.2 29.6 - - - -
147C LYS* 1.3 74.8 - - - +
149C HIS* 1.3 66.0 + - - +
150C TYR* 3.6 21.4 - - + +
175D ARG* 3.4 30.7 - - + -
176D ASN* 3.5 15.5 - - - -
177D GLY* 3.8 17.5 - - - -
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Residues in contact with HIS 149 (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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106C ILE* 3.6 4.3 - - - +
107C CYS* 2.8 46.7 + - + +
109C ILE* 4.1 4.8 - - - +
119C VAL* 3.3 50.0 + - + +
121C TRP* 3.5 18.4 - + - +
132C VAL* 6.5 0.7 - - + -
133C SER 3.7 4.9 - - - -
134C GLU* 3.3 28.2 + - + -
147C LYS* 3.2 39.5 + - + +
148C PHE* 1.3 78.1 + - - +
150C TYR* 1.3 62.7 + - - +
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Residues in contact with TYR 150 (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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44C ARG* 3.4 22.6 + - - -
94C ARG* 5.9 0.2 - - - -
104C ILE* 4.0 23.6 - - + -
105C LEU 3.5 2.0 - - - +
106C ILE* 4.0 17.7 - - + -
121C TRP* 3.4 7.5 + - - -
131C GLY 4.2 1.8 - - - +
132C VAL* 3.1 7.3 - - - -
133C SER* 2.9 58.6 + - - +
134C GLU* 4.5 1.3 - - - -
135C THR* 3.9 14.3 - - + +
148C PHE* 3.6 18.7 - - + +
149C HIS* 1.3 79.0 - - - +
151C LEU* 1.3 61.1 + - - +
176D ASN 2.7 29.1 + - - -
177D GLY* 3.2 21.3 - - - -
178D ASP* 3.6 10.3 + - + -
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Residues in contact with LEU 151 (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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104C ILE* 4.5 2.9 - - - +
105C LEU* 2.8 41.9 + - + +
121C TRP* 3.6 40.4 - - + -
122C LEU 5.2 1.1 - - - +
123C ARG* 5.4 2.5 - - - +
128C VAL* 3.9 17.9 - - + -
130C GLU 3.8 13.5 - - - +
131C GLY 3.6 1.3 - - - +
132C VAL* 3.7 22.9 - - + -
150C TYR* 1.3 75.5 - - - +
152C THR* 1.3 77.6 + - - +
153C PHE* 3.5 0.7 + - + -
161C TYR* 3.7 33.7 - - + -
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Residues in contact with THR 152 (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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103C ASN 3.8 8.1 - - - +
104C ILE* 4.4 16.6 - - + -
123C ARG* 4.9 6.6 + - - -
130C GLU 4.3 1.4 + - - -
131C GLY* 3.1 35.6 + - - +
151C LEU* 1.3 86.4 - - - +
153C PHE* 1.3 61.1 + - - +
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Residues in contact with PHE 153 (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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93C SER* 4.7 4.5 - - - -
97C VAL* 4.7 1.6 - - + -
102C PRO* 3.9 2.0 - - - +
103C ASN* 3.0 51.3 + - + -
104C ILE 3.2 30.5 - - - -
105C LEU* 3.5 26.0 - - + -
123C ARG* 5.8 3.1 - - - +
151C LEU* 3.8 2.5 - - + +
152C THR* 1.3 76.9 - - - +
154C LEU* 1.3 60.9 + - - +
155C PRO* 3.5 24.4 - - + +
161C TYR* 3.5 39.5 - + + +
178C TRP* 3.8 33.0 - + - -
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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