Contacts of the strand formed by residues 125 - 135 (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 TYR 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A VAL* 4.2 12.8 - - + -
78A GLY* 3.4 28.0 - - - -
79A ILE* 4.4 26.3 - - + +
95A ASP 5.3 0.4 - - - -
96A ASP* 6.2 0.9 - - - -
97A MET* 5.0 2.9 - - - +
123A GLU 4.0 1.3 + - - -
124A THR* 1.3 77.6 - - - +
126A VAL* 1.3 64.3 + - - +
149A LEU* 3.0 29.4 + - + +
152A MET* 3.4 42.4 - - + -
155A PHE* 4.2 17.7 - + - -
11B ARG* 3.2 10.4 + - - -
68B GLU* 2.6 39.6 + - - -
85B VAL* 4.7 10.3 - - + -
87B PHE* 4.0 9.9 - + - -
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Residues in contact with VAL 126 (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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76A ILE 4.0 0.2 - - - +
77A VAL* 3.3 5.9 - - - +
78A GLY 2.8 31.3 + - - +
80A ILE* 3.6 26.0 - - + -
94A ILE* 4.8 3.1 - - + -
120A VAL* 4.2 6.1 - - + -
124A THR* 3.3 23.6 - - + +
125A TYR* 1.3 82.5 - - - +
127A LYS* 1.3 67.6 + - - +
128A VAL* 4.0 10.9 - - + +
146A ILE* 2.9 36.3 - - + -
147A MET 3.8 9.2 - - - +
148A PRO* 4.2 2.7 - - + -
149A LEU* 4.3 5.8 - - - +
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Residues in contact with LYS 127 (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* 4.1 27.3 - - - +
76A ILE 3.5 9.0 - - - +
77A VAL* 4.0 14.6 - - + -
126A VAL* 1.3 75.8 - - - +
128A VAL* 1.3 65.2 + - - +
146A ILE* 3.4 4.9 - - - -
147A MET* 2.9 62.2 + - + +
149A LEU* 4.3 10.6 - - + +
154A GLU* 4.9 13.7 + - + +
158A HIS* 4.5 8.9 - - + -
161A GLU* 4.5 12.1 + - - -
151C ASP* 5.8 1.6 + - - -
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Residues in contact with VAL 128 (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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74A VAL 3.6 0.3 - - - +
75A THR* 2.9 29.4 - - - -
76A ILE* 2.8 27.3 + - + +
94A ILE* 3.6 31.6 - - + -
104A VAL* 4.1 20.9 - - + -
126A VAL* 4.0 11.7 - - + +
127A LYS* 1.3 82.0 - - - +
129A ALA* 1.3 72.1 + - - +
130A GLY 4.4 0.4 - - - +
141A LEU* 4.4 18.8 - - + -
143A ALA* 4.2 7.0 - - + -
145A LYS 3.5 2.9 - - - +
146A ILE* 4.1 9.2 - - + -
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Residues in contact with ALA 129 (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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46A ILE* 5.7 2.2 - - + -
73A GLN* 6.3 1.6 - - - +
74A VAL 3.5 4.9 - - - +
75A THR* 4.2 14.4 - - + -
127A LYS 4.3 0.2 - - - -
128A VAL* 1.3 76.1 - - - +
130A GLY* 1.3 50.9 + - - +
143A ALA* 3.5 2.1 - - - -
144A PHE* 2.7 33.5 + - + -
145A LYS* 2.9 41.9 + - + +
147A MET* 4.5 4.8 - - + +
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Residues in contact with GLY 130 (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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73A GLN* 3.5 4.2 - - - +
74A VAL* 2.9 38.5 + - - +
128A VAL* 4.1 4.0 - - - +
129A ALA* 1.3 75.5 - - - +
131A HIS* 1.3 65.3 + - - -
141A LEU* 4.7 3.8 - - - +
142A VAL 2.9 15.7 - - - -
143A ALA* 3.9 3.4 - - - -
144A PHE* 4.1 7.4 - - - -
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Residues in contact with HIS 131 (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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72A SER* 3.7 14.4 + - - +
73A GLN* 3.5 34.2 + - + +
130A GLY* 1.3 77.1 - - - -
132A LEU* 1.3 63.2 + - - +
133A ARG* 3.4 32.0 + - - +
141A LEU* 3.4 5.5 - - - +
142A VAL* 2.7 35.0 + - + +
144A PHE* 3.0 41.9 - + + -
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Residues in contact with LEU 132 (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* 4.1 39.7 - - + +
57A ALA* 4.4 12.8 - - + -
64A PHE* 3.6 52.9 - - + -
71A ILE* 4.8 9.0 - - + -
72A SER* 3.0 22.1 + - - +
74A VAL* 5.2 0.2 - - + -
102A MET* 5.0 0.7 - - + -
131A HIS* 1.3 73.0 - - - +
133A ARG* 1.3 83.4 + - - +
139A LYS* 4.5 14.8 - - + +
140A SER 3.8 10.1 - - - +
141A LEU* 3.6 12.3 - - + +
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Residues in contact with ARG 133 (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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64A PHE* 3.9 6.7 - - - -
131A HIS* 3.4 36.0 + - - +
132A LEU* 1.3 86.4 + - - +
134A SER* 1.3 64.1 + - - +
135A PHE* 4.6 24.8 - - + -
138A LYS 4.5 0.2 - - - -
139A LYS* 3.4 4.2 - - - -
140A SER* 2.8 40.3 + - - +
142A VAL* 3.0 46.0 - - + +
144A PHE* 5.9 3.2 - - - -
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Residues in contact with SER 134 (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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59A LEU* 3.8 19.4 - - - +
64A PHE* 3.6 21.8 - - - -
133A ARG* 1.3 79.6 - - - +
135A PHE* 1.3 75.4 + - - +
137A ASN* 3.9 10.8 + - - -
138A LYS 3.3 24.1 + - - -
139A LYS* 4.1 8.5 + - - +
140A SER* 5.6 0.2 - - - -
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Residues in contact with PHE 135 (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* 4.8 24.2 - - - -
133A ARG* 4.6 31.9 - - + -
134A SER* 1.3 91.2 - - - +
136A GLN* 1.3 76.8 + - + +
137A ASN 3.2 1.1 - - - -
138A LYS* 2.9 24.8 + - - +
140A SER* 5.5 1.6 - - - -
142A VAL* 5.6 2.5 - - + -
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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