Contacts of the strand formed by residues 145 - 153 (chain A) in PDB entry 1JK8
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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10A VAL* 4.8 13.7 - - + -
12A LEU* 3.9 25.4 - - + -
21A GLN* 5.2 1.1 - - - -
111A ASN* 3.5 5.2 + - - -
112A ILE* 2.8 43.2 + - + +
113A PHE* 4.3 1.8 - + - -
115A PRO* 4.0 28.3 - - + -
137A PHE* 3.6 38.8 - + + -
138A LEU 3.1 20.9 - - - +
139A SER* 4.2 7.2 - - - -
140A LYS* 3.9 6.0 - - - +
143A HIS 3.9 6.1 - - - -
144A SER* 1.3 78.1 - - - +
146A PHE* 1.3 65.3 + - - +
10B GLN* 3.1 41.5 - - + -
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Residues in contact with PHE 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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28A GLY* 4.4 5.6 - - - -
108A LEU* 4.0 16.6 - - + -
109A VAL 3.2 14.4 - - - +
110A ASP* 3.7 17.5 - - - +
112A ILE* 4.1 2.2 - - - -
137A PHE* 3.8 0.4 - - - -
138A LEU* 2.8 65.4 + - + +
139A SER 4.0 8.7 - - - -
140A LYS* 3.4 23.8 - - + -
145A PHE* 1.3 77.8 - - - +
147A LYS* 1.3 63.5 + - - +
148A ILE* 3.8 25.4 - - + -
149B ARG* 4.2 24.0 - - - -
151B GLY* 6.1 0.4 - - - -
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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 3.9 0.7 - - - +
108A LEU* 4.0 0.2 - - - +
109A VAL* 2.9 35.3 + - - +
112A ILE* 3.7 12.5 - - + +
117A VAL* 3.9 7.2 - - + -
119A ILE* 3.4 19.5 - - + -
134A GLU* 3.0 35.5 + - - +
135A THR* 2.9 35.7 + - - +
136A SER* 3.8 15.2 - - - +
137A PHE* 3.6 38.1 - - + +
146A PHE* 1.3 76.0 - - - +
148A ILE* 1.3 70.9 + - - +
149A SER 4.3 0.2 + - - -
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Residues in contact with ILE 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* 3.6 24.5 - - + -
107A CYS 3.4 3.4 - - - +
108A LEU* 4.0 23.3 - - + -
134A GLU* 3.2 4.0 - - - +
135A THR* 2.8 46.6 + - + +
146A PHE* 3.8 23.8 - - + -
147A LYS* 1.3 79.0 - - - +
149A SER* 1.3 62.5 + - - +
150A TYR* 3.6 25.5 - - + -
149B ARG* 3.7 17.0 - - + +
150B ASN 3.6 13.7 - - - +
151B GLY* 4.0 10.3 - - - -
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Residues in contact with SER 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* 3.7 3.1 - - - -
107A CYS* 2.9 35.7 + - - -
119A ILE* 3.4 33.9 + - - +
121A TRP* 2.6 35.6 + - - -
132A VAL* 4.2 3.6 - - - +
133A SER 3.2 11.3 + - - -
134A GLU* 4.0 7.6 - - - +
147A LYS 4.3 0.2 - - - -
148A ILE* 1.3 74.5 - - - +
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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94A LYS* 6.2 1.8 - - + -
104A THR* 4.2 15.3 - - + -
105A LEU 3.5 1.8 - - - -
106A ILE* 4.0 24.7 - - + -
121A TRP* 3.6 7.4 + - - -
131A GLY 4.0 2.2 - - - +
132A VAL* 3.1 6.2 - - - -
133A SER* 2.6 59.9 + - - +
134A GLU* 4.2 1.8 - - - -
135A THR* 3.8 13.0 - - + +
148A ILE* 3.6 25.9 - - + +
149A SER* 1.3 76.7 + - - +
151A LEU* 1.3 61.1 + - - +
152A THR* 6.0 1.3 - - + -
150B ASN* 2.5 31.2 + - + -
151B GLY* 3.2 21.1 - - - -
152B ASP* 3.3 13.4 + - + -
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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 THR* 4.0 2.0 - - - -
105A LEU* 2.8 38.5 + - + -
121A TRP* 3.7 38.4 - - + -
122A LEU 5.5 0.2 - - - +
128A VAL* 3.6 31.6 - - + -
130A GLU 3.9 6.5 - - - +
131A GLY 3.5 1.1 - - - -
132A VAL* 3.8 13.2 - - + -
150A TYR* 1.3 75.0 - - - +
152A THR* 1.3 76.6 + - - +
153A PHE* 3.5 5.3 + - + -
161A TYR* 3.7 35.7 - - + -
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Residues in contact with THR 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 8.3 - - - +
104A THR* 3.9 19.1 - - + +
130A GLU 5.1 0.5 - - - +
131A GLY* 3.0 32.8 + - - +
150A TYR* 6.0 2.0 - - + -
151A LEU* 1.3 85.3 - - - +
153A PHE* 1.3 61.4 + - - +
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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 SER* 5.2 0.9 - - - -
97A VAL* 4.8 1.8 - - + -
102A PRO* 3.7 2.8 - - - +
103A ASN* 2.8 49.7 + - + +
104A THR 3.5 15.3 - - - -
105A LEU* 3.4 27.8 - - + -
151A LEU* 3.5 17.5 - - + +
152A THR* 1.3 75.8 - - - +
154A LEU* 1.3 60.1 + - - +
155A PRO* 3.4 27.8 - - + +
159A GLU* 5.5 0.2 - - - +
161A TYR* 3.3 38.1 - + + +
178A TRP* 3.9 36.6 - + - -
180A PRO* 5.6 0.9 - - + -
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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