Contacts of the strand formed by residues 145 - 153 (chain A) in PDB entry 1R5I
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.9 24.7 - + - -
111A LYS 3.2 24.3 + - - -
112A PHE* 2.7 47.3 + - + +
113A THR* 3.7 12.8 - - - -
115A PRO* 3.6 38.4 - - + -
137A PHE* 4.0 19.7 - - + -
138A LEU 3.3 19.1 - - - +
139A PRO* 4.6 4.7 - - + -
140A ARG* 3.8 5.4 - - - +
143A HIS 4.1 7.4 - - - -
144A LEU* 1.3 79.3 - - - +
146A ARG* 1.3 59.6 + - - +
8B LEU* 3.9 7.0 - - + -
10B GLN* 3.4 30.5 - - - -
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Residues in contact with ARG 146 (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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25A ASP* 4.9 1.0 + - - -
28A GLY* 2.8 35.6 + - - -
109A ILE 3.5 6.3 - - - +
110A ASP* 3.2 30.7 - - + +
112A PHE* 4.4 1.3 - - - -
137A PHE* 3.7 2.6 - - - -
138A LEU* 2.8 51.6 + - + +
139A PRO 4.3 12.3 + - - -
140A ARG* 3.9 15.5 - - + +
145A PHE* 1.3 72.6 - - - +
147A LYS* 1.3 64.4 + - - +
148A PHE* 4.2 25.6 - - + -
149B GLN* 2.8 29.3 + - - +
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Residues in contact with LYS 147 (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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107A CYS 3.8 0.5 - - - +
108A PHE* 3.8 1.2 - - - +
109A ILE* 3.0 47.3 + - + +
112A PHE* 4.3 6.7 - - + -
117A VAL* 4.0 10.8 - - + -
134A GLU* 2.9 29.7 + - - +
135A THR* 2.7 35.8 + - - +
136A VAL* 4.0 5.0 - - - +
137A PHE* 3.4 45.5 - - + -
146A ARG* 1.3 75.6 - - - +
148A PHE* 1.3 71.9 + - - +
149A HIS* 3.6 21.6 - - + +
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Residues in contact with PHE 148 (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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106A ILE* 3.9 8.5 - - + -
107A CYS 3.5 3.8 - - - -
108A PHE* 3.3 30.3 - + + -
134A GLU* 3.1 5.6 - - - +
135A THR* 2.9 40.3 + - + +
138A LEU* 3.9 25.8 - - + -
146A ARG* 4.2 28.5 - - + -
147A LYS* 1.3 81.6 - - - +
149A HIS* 1.3 63.6 + - - +
150A TYR* 3.5 20.2 - - + +
149B GLN* 3.1 29.2 - - + -
150B ASN 3.2 17.3 - - - -
151B GLY* 3.6 19.7 - - - -
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Residues in contact with HIS 149 (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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106A ILE* 3.5 4.0 - - - +
107A CYS* 2.9 39.5 + - + -
109A ILE* 4.1 6.7 - - - +
117A VAL* 5.3 0.2 - - + -
119A VAL* 3.4 48.8 + - + +
121A TRP* 3.4 26.1 - + + +
132A VAL* 6.2 3.4 - - + -
133A SER 3.5 6.3 - - - -
134A GLU* 3.0 27.7 + - + -
147A LYS* 3.6 33.5 - - + +
148A PHE* 1.3 78.0 + - - +
150A TYR* 1.3 63.5 + - - +
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Residues in contact with TYR 150 (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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44A ARG* 3.6 19.1 - - - -
104A VAL* 4.1 13.9 - - + -
105A LEU 3.4 3.1 - - - -
106A ILE* 3.8 31.9 - - + -
121A TRP* 3.7 2.7 + - - -
132A VAL* 3.2 29.5 - - - +
133A SER* 2.8 40.7 + - - +
134A GLU* 4.5 0.9 - - - -
135A THR* 3.7 16.6 - - + +
148A PHE* 3.5 13.5 - - + +
149A HIS* 1.3 76.9 - - - +
151A LEU* 1.3 60.4 + - - +
152A PRO* 4.1 4.0 - - + -
150B ASN 2.5 29.9 + - - -
151B GLY* 3.1 21.1 + - - -
152B ASP* 4.4 13.5 - - + -
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Residues in contact with LEU 151 (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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104A VAL* 3.9 1.3 - - - +
105A LEU* 2.8 42.3 + - + -
121A TRP* 3.7 35.9 - - + +
123A ARG* 5.1 4.3 - - - +
128A VAL* 3.4 37.9 - - + -
130A THR 4.3 7.4 - - - +
132A VAL* 3.4 14.4 - - + -
150A TYR* 1.3 75.1 - - - +
152A PRO* 1.3 85.4 - - + +
153A PHE* 3.5 7.6 - - + -
161A TYR* 3.9 26.9 - - + -
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Residues in contact with PRO 152 (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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103A ASN 3.5 10.8 - - - +
104A VAL* 4.1 14.4 - - + -
123A ARG* 5.3 2.1 + - - -
130A THR 5.2 1.6 - - - +
131A GLY* 3.3 37.7 - - - +
150A TYR* 4.0 3.1 - - + +
151A LEU* 1.3 96.4 - - + +
153A PHE* 1.3 61.0 + - - +
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Residues in contact with PHE 153 (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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93A THR* 4.2 5.8 - - + -
97A VAL* 4.7 0.4 - - + -
102A PRO* 3.7 2.4 - - - +
103A ASN* 2.9 48.5 + - + +
104A VAL 3.6 13.7 - - - -
105A LEU* 3.4 34.1 - - + -
123A ARG* 4.9 4.3 - - - +
151A LEU* 3.5 16.8 - - + +
152A PRO* 1.3 76.5 - - - +
154A LEU* 1.3 67.6 + - - +
155A PRO* 3.4 27.1 - - + +
161A TYR* 3.6 37.5 - + + +
178A TRP* 3.8 34.3 - + - -
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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