Contacts of the helix formed by residues 122 - 131 (chain A) in PDB entry 2P6U
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 SER 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A VAL* 3.7 19.1 - - - +
75A VAL 2.9 14.6 + - - -
76A PRO* 3.8 12.6 - - - +
121A THR* 1.3 72.7 - - - +
123A GLU* 1.3 60.8 + - - +
125A ALA* 3.2 3.3 + - - +
126A ASP* 2.9 27.9 + - - +
155A ARG* 5.5 4.8 - - - +
158A THR* 4.3 16.6 - - - +
159A LEU* 4.0 17.9 - - - +
162A LEU* 3.7 15.5 - - - +
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Residues in contact with GLU 123 (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 PRO 5.5 2.2 - - - +
78A ARG* 2.7 38.1 + - - +
105A TYR* 3.8 18.8 + - - +
121A THR* 3.2 5.1 - - - +
122A SER* 1.3 77.2 - - - +
124A LYS* 1.3 55.6 + - - +
126A ASP* 3.0 3.7 + - - +
127A SER* 2.7 34.8 + - - -
155A ARG* 5.0 5.8 + - - +
158A THR* 4.4 11.0 + - + +
487A TYR* 3.2 38.3 + - + +
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Residues in contact with LYS 124 (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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101A SER* 2.9 44.4 - - - +
102A THR* 4.5 3.8 - - + -
103A GLY 4.6 7.0 - - - +
104A ASP* 2.3 37.2 + - - +
105A TYR* 4.0 21.1 + - + +
107A SER 3.7 7.3 + - - -
109A ASP* 3.3 16.9 + - - -
120A THR* 3.7 5.6 - - - +
121A THR* 3.1 21.8 + - - +
123A GLU* 1.3 78.3 - - - +
125A ALA* 1.3 50.4 + - - +
127A SER* 3.4 0.8 + - - -
128A LEU* 2.7 70.6 + - + +
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Residues in contact with ALA 125 (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 LEU* 4.5 13.0 - - + -
74A VAL* 4.1 10.3 - - + -
120A THR* 3.7 5.8 + - - +
121A THR 2.8 12.5 + - - +
122A SER 3.3 9.2 - - - +
124A LYS* 1.3 74.8 - - - +
126A ASP* 1.3 67.9 + - - +
128A LEU* 3.1 13.8 + - - +
129A ILE* 2.9 29.6 + - + +
136A ILE* 4.3 0.6 - - - +
162A LEU* 3.8 23.3 - - + -
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Residues in contact with ASP 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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122A SER 2.9 13.8 + - - +
123A GLU 3.0 6.9 + - - +
125A ALA* 1.3 74.4 - - - +
127A SER* 1.3 64.2 + - - +
129A ILE* 3.0 13.8 + - - +
130A ARG* 2.8 45.4 + - - -
158A THR* 3.9 12.4 - - + +
161A ILE* 5.5 2.5 - - - -
162A LEU* 4.3 8.4 - - + +
165A LYS* 2.7 36.9 + - - +
418A HIS* 4.2 8.4 + - - -
487A TYR* 3.1 18.0 + - - +
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Residues in contact with SER 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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105A TYR* 3.2 45.7 + - - +
123A GLU 2.7 13.4 + - - -
124A LYS* 3.4 8.1 - - - -
126A ASP* 1.3 70.0 - - - +
128A LEU* 1.3 68.6 + - - +
130A ARG* 2.7 6.3 + - - +
131A ASN* 2.7 42.8 + - - +
485A ARG 4.6 1.2 + - - -
487A TYR* 4.1 15.6 - - - -
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Residues in contact with LEU 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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72A LEU* 5.9 0.4 - - + -
101A SER* 5.0 0.9 - - - +
107A SER 4.3 3.8 - - - +
108A ARG 3.9 19.1 - - - +
109A ASP* 4.1 9.0 - - + +
112A LEU* 4.9 0.9 - - + -
120A THR* 4.5 8.5 - - + +
124A LYS* 2.7 71.2 + - + +
125A ALA* 3.1 11.9 + - - +
127A SER* 1.3 72.5 + - - +
129A ILE* 1.3 59.2 + - - +
131A ASN* 3.5 6.8 - - - -
132A ARG 3.2 3.8 + - - -
133A ALA* 2.9 30.4 + - + -
135A TRP* 3.5 35.9 - - + +
136A ILE* 3.5 13.7 - - + -
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Residues in contact with ILE 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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125A ALA* 2.9 21.6 + - + +
126A ASP* 3.1 18.4 - - - +
127A SER 2.8 1.4 + - - -
128A LEU* 1.3 75.0 - - - +
130A ARG* 1.3 66.8 + - - +
132A ARG* 2.8 18.6 + - - +
136A ILE* 3.2 25.6 - - + -
162A LEU* 3.8 28.0 - - + +
165A LYS* 3.9 17.7 - - + +
166A MET* 4.0 15.0 - - + -
169A MET* 4.4 9.0 - - - -
425A ASP* 4.1 4.5 - - + +
427A TYR* 3.5 25.1 - - - +
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Residues in contact with ARG 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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126A ASP* 2.8 53.9 + - - -
127A SER 2.7 9.6 + - - +
129A ILE* 1.3 73.6 - - - +
131A ASN* 1.3 62.5 + - - +
132A ARG* 3.0 15.2 + - - +
165A LYS* 3.7 1.1 - - - +
417A PHE* 3.4 37.4 + - - -
418A HIS* 4.5 2.4 + - - -
420A LEU* 6.0 2.0 - - - +
421A SER* 3.5 31.4 + - - +
425A ASP* 3.1 35.3 - - - +
483A VAL 5.0 0.8 + - - -
484A SER* 3.3 42.5 + - - +
485A ARG* 4.7 8.4 - - + +
487A TYR* 3.2 25.5 - - - +
488A ILE 5.0 1.8 + - - -
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Residues in contact with ASN 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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105A TYR 3.6 9.5 + - - -
106A GLU* 3.0 34.5 - - - +
107A SER 4.1 15.9 + - - +
108A ARG* 3.0 28.2 + - + +
127A SER* 2.7 50.3 + - - +
128A LEU 3.5 3.6 - - - +
130A ARG* 1.3 73.8 - - - +
132A ARG* 1.3 67.7 + - - +
133A ALA 3.4 1.6 - - - -
485A ARG* 3.4 24.3 + - - +
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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