Contacts of the strand formed by residues 139 - 144 (chain A) in PDB entry 3I7P
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 LEU 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ASP* 4.3 8.7 - - + +
112A ILE* 4.3 25.4 - - + +
113A GLY* 5.1 0.7 - - - -
133A LEU 4.6 0.9 - - - +
134A ARG* 4.4 7.3 - - - +
136A TYR* 3.0 39.6 + - + +
137A ASP 2.9 8.6 + - - +
138A GLY* 1.3 82.9 + - - +
140A PHE* 1.3 62.4 + - - +
141A LYS 4.1 0.2 - - - -
156A ASN* 3.3 42.0 - - + +
157A ILE 3.5 11.0 - - - +
158A ARG* 4.5 9.4 - - + +
159A LEU* 4.2 6.8 - - - +
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Residues in contact with PHE 140 (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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123A ILE* 4.5 12.8 - - + -
130A MET* 5.6 0.2 - - - -
132A GLY* 3.6 20.9 - - - -
133A LEU 3.3 24.7 - - - -
134A ARG* 4.8 9.0 - - + -
139A LEU* 1.3 76.0 - - - +
141A LYS* 1.3 62.3 + - - +
142A VAL* 3.5 26.1 + - + +
156A ASN* 3.6 4.4 - - - -
157A ILE* 3.0 34.6 + - + +
159A LEU* 3.9 19.3 - - + -
167A VAL* 4.9 7.4 - - + -
169A PHE* 4.7 4.3 - + - -
178A ILE* 4.1 31.6 - - + -
195A VAL* 4.8 7.9 - - + -
202A PHE* 4.1 22.0 - + + -
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Residues in contact with LYS 141 (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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108A VAL* 2.6 27.1 + - + +
109A GLN 4.1 0.4 + - - -
110A ASP* 2.5 43.1 + - - -
132A GLY* 3.5 1.7 - - - -
133A LEU* 3.0 59.8 + - + -
135A LEU* 4.0 9.8 - - + +
136A TYR* 5.7 0.9 - - - -
139A LEU 4.1 0.2 - - - -
140A PHE* 1.3 74.2 - - - +
142A VAL* 1.3 67.0 + - - +
143A ILE* 4.3 1.1 - - + -
154A ALA* 3.4 31.6 + - + +
155A PHE 3.3 15.5 - - - +
156A ASN* 3.2 16.9 + - - +
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Residues in contact with VAL 142 (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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130A MET* 3.7 32.3 - - + -
131A ILE 3.4 4.5 - - - +
140A PHE* 3.5 28.3 - - + +
141A LYS* 1.3 79.2 - - - +
143A ILE* 1.3 69.4 + - - +
144A PRO* 3.3 9.6 - - + +
154A ALA* 3.1 21.9 - - - +
155A PHE* 2.9 44.1 + - + -
157A ILE* 4.7 2.0 - - + -
195A VAL* 4.6 10.1 - - + -
197A LEU* 5.3 3.4 - - + -
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Residues in contact with ILE 143 (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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78A PHE* 4.8 7.2 - - + -
86A ALA* 4.6 7.9 - - + -
108A VAL* 3.8 23.8 - - + -
131A ILE* 2.9 47.0 + - + +
133A LEU* 4.1 17.9 - - + +
141A LYS 4.3 0.2 - - - -
142A VAL* 1.3 72.8 - - - +
144A PRO* 1.4 73.3 - - - +
145A LEU* 3.6 5.1 + - + +
149A ASN* 4.1 1.8 - - - +
152A LEU* 3.4 42.0 - - + +
153A LYS 3.9 9.4 - - - +
154A ALA* 3.5 20.0 - - + -
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Residues in contact with PRO 144 (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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129A ARG 3.9 7.0 - - - +
130A MET* 4.1 4.5 - - + -
142A VAL* 3.3 13.2 - - + +
143A ILE* 1.4 84.9 - - - +
145A LEU* 1.3 63.5 + - - +
146A ASP* 4.3 10.7 - - - +
149A ASN* 2.5 35.3 + - - +
153A LYS 3.5 14.8 - - - +
154A ALA* 4.4 1.8 - - - -
155A PHE* 4.1 20.9 - - + -
197A LEU* 4.0 20.0 - - + -
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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