Contacts of the strand formed by residues 138 - 148 (chain A) in PDB entry 2PQA
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 LYS 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ASP* 2.7 30.5 + - - +
105A ARG* 6.4 0.2 - - - +
133A ARG 4.5 0.2 - - - -
134A SER* 3.3 5.9 + - - -
135A PHE 2.9 35.7 + - - +
136A GLN* 4.1 3.8 - - + +
137A ASN* 1.3 72.2 - - - +
139A LYS* 1.3 71.8 + - - +
140A SER* 3.8 5.4 + - - -
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Residues in contact with LYS 139 (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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54A LEU 2.7 25.2 + - - +
55A LEU* 3.0 26.2 + - + -
57A ALA* 2.5 34.0 + - - +
58A THR* 5.5 0.2 - - - +
59A LEU* 5.6 2.5 - - - -
64A PHE* 4.1 24.1 - - + -
102A MET* 3.7 28.6 - - + +
103A ASP* 4.7 3.3 + - - +
132A LEU* 4.5 6.5 - - + +
133A ARG 3.4 10.1 - - - +
134A SER* 4.2 8.3 - - - +
137A ASN 4.0 4.2 + - - +
138A LYS* 1.3 79.9 + - - +
140A SER* 1.3 65.7 + - - +
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Residues in contact with SER 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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102A MET* 3.9 8.4 - - - +
103A ASP* 3.3 24.5 - - - -
105A ARG* 2.9 33.8 + - - -
132A LEU* 3.7 4.6 - - - +
133A ARG* 2.8 41.5 + - - +
135A PHE* 5.5 2.6 - - - -
138A LYS* 4.6 5.3 + - - -
139A LYS* 1.3 77.5 - - - +
141A LEU* 1.3 63.4 + - - +
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Residues in contact with LEU 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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51A ILE* 6.2 0.4 - - + -
54A LEU* 4.1 13.0 - - + -
74A VAL* 3.5 30.1 - - + +
76A ILE* 4.0 26.7 - - + -
102A MET* 4.0 11.0 - - + -
103A ASP 2.9 7.9 + - - +
104A VAL* 3.3 24.6 - - + -
105A ARG* 2.9 30.7 + - - -
128A VAL* 4.4 11.7 - - + -
130A GLY 5.3 1.6 - - - +
131A HIS 3.4 16.8 - - - +
132A LEU* 3.6 18.4 - - + -
140A SER* 1.3 75.7 - - - +
142A VAL* 1.3 67.4 + - - +
143A ALA 3.9 0.2 - - - -
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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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105A ARG* 4.0 15.5 - - - +
107A TRP* 3.6 30.5 - - + -
130A GLY* 2.9 3.4 - - - -
131A HIS 2.7 36.9 + - - +
133A ARG* 3.0 52.9 - - + +
135A PHE* 5.6 4.0 - - + -
141A LEU* 1.3 73.8 - - - +
143A ALA* 1.3 59.5 + - - +
144A PHE* 3.9 16.9 - - + -
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Residues in contact with ALA 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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104A VAL* 3.7 20.6 - - + -
105A ARG 2.9 21.0 + - - +
106A GLN* 3.2 14.5 - - - +
107A TRP* 4.0 11.8 - - - -
128A VAL* 4.2 4.7 - - + -
129A ALA 3.5 8.7 - - - +
130A GLY* 3.9 1.8 - - - -
141A LEU 3.9 0.2 - - - -
142A VAL* 1.3 73.9 - - - +
144A PHE* 1.3 66.2 + - - +
146A ILE* 3.8 25.1 - - + -
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLN* 5.8 1.8 - - - -
106A GLN* 4.6 7.6 + - - +
129A ALA* 2.7 14.4 + - + +
130A GLY* 4.1 3.4 - - - -
131A HIS* 3.0 48.2 - + + -
133A ARG* 5.9 2.9 - - - -
142A VAL* 3.9 20.2 - - + -
143A ALA* 1.3 78.4 - - - +
145A LYS* 1.3 62.9 + - + +
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Residues in contact with LYS 145 (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 GLN* 4.6 3.4 - - - +
128A VAL* 3.5 1.0 - - - +
129A ALA* 2.9 50.4 + - + +
144A PHE* 1.3 81.3 - - + +
146A ILE* 1.3 69.2 + - - +
147A MET* 4.0 31.8 - - + +
153C ASN* 4.5 12.5 + - - +
95D ASP* 3.6 32.7 + - - +
98D LEU* 4.6 12.6 - - - +
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Residues in contact with ILE 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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80A ILE* 4.9 2.0 - - + -
92A TYR* 3.7 25.4 - - + -
94A ILE* 5.3 0.9 - - + -
104A VAL* 4.2 7.2 - - + -
106A GLN* 3.4 45.1 + - + +
120A VAL* 4.5 19.3 - - + +
126A VAL* 2.9 32.1 - - + -
127A LYS 3.4 3.6 - - - -
128A VAL* 4.1 9.4 - - + -
143A ALA* 3.8 17.9 - - + -
145A LYS* 1.3 79.9 - - - +
147A MET* 1.3 58.0 - - - +
148A PRO* 3.3 10.2 - - - +
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Residues in contact with MET 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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75A THR* 6.3 0.2 - - + -
126A VAL* 4.4 1.1 - - - -
127A LYS* 2.9 80.3 + - + +
128A VAL 4.4 0.7 - - - +
129A ALA* 4.5 7.0 - - + +
145A LYS* 4.2 46.7 - - + +
146A ILE* 1.3 70.1 - - - +
148A PRO* 1.3 70.4 - - + +
149A LEU* 3.5 2.3 + - - +
92D HIS* 4.7 24.5 - - + +
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Residues in contact with PRO 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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120A VAL* 4.4 24.9 - - + -
124A THR* 4.4 13.2 - - + -
125A TYR 3.6 10.3 - - - +
126A VAL* 4.2 3.8 - - + -
146A ILE 3.3 11.2 - - - +
147A MET* 1.3 87.4 - - + +
149A LEU* 1.3 64.2 + - - +
150A GLU* 3.5 22.0 + - - +
92D HIS* 5.1 6.4 + - - -
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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