Contacts of the helix formed by residues 110 - 126 (chain A) in PDB entry 2P1N
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 ILE 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLU* 3.8 15.9 - - + +
26A SER* 3.5 16.8 - - - +
55A VAL* 4.0 17.7 - - + -
58A TYR* 4.8 5.2 - - + -
59A CYS* 4.1 21.5 - - - -
105A ALA* 2.9 14.2 + - - +
108A LEU* 3.4 45.1 - - + +
109A ASN* 1.3 71.2 - - - +
111A LYS* 1.3 64.9 + - - +
112A ASN* 4.7 6.1 - - - +
113A LEU* 3.1 40.5 + - + +
114A LEU* 3.1 13.5 + - - +
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Residues in contact with LYS 111 (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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25A GLU 5.0 0.6 + - - -
27A GLN* 4.3 14.0 - - - +
109A ASN 3.6 5.2 + - - -
110A ILE* 1.3 70.9 - - - +
112A ASN* 1.3 69.8 + - - +
113A LEU 2.9 2.1 + - - -
114A LEU* 3.2 13.1 + - + +
115A ASP* 3.1 43.7 + - - +
16B HIS* 6.2 3.4 - - + -
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Residues in contact with ASN 112 (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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25A GLU* 4.7 13.6 + - - +
58A TYR* 3.0 41.5 + - - +
62A HIS* 4.3 14.2 - - + +
110A ILE* 3.5 4.9 + - - +
111A LYS* 1.3 80.7 + - - +
113A LEU* 1.3 55.4 + - - +
115A ASP* 3.5 11.6 + - + +
116A LEU* 3.1 22.2 + - - +
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Residues in contact with LEU 113 (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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55A VAL* 4.1 25.8 - - + -
58A TYR* 3.6 46.1 + - + -
59A CYS* 5.9 0.2 - - - -
90A PHE* 4.4 9.0 - - + -
91A MET* 4.8 0.7 - - + -
101A LEU* 4.2 15.7 - - + -
105A ALA* 3.0 28.7 - - + -
110A ILE* 3.1 22.8 + - + +
111A LYS 2.9 1.4 + - - -
112A ASN* 1.3 73.3 - - - +
114A LEU* 1.3 55.0 + - - +
115A ASP 3.3 0.2 - - - -
116A LEU* 4.3 2.5 - - + +
117A THR* 2.7 59.8 + - + +
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Residues in contact with LEU 114 (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 ILE* 4.0 15.3 - - + +
105A ALA* 3.6 5.4 - - + +
106A ASN* 3.3 52.9 - - + +
109A ASN* 6.4 1.1 - - - -
110A ILE 3.1 11.8 + - - +
111A LYS* 3.5 17.9 - - + +
113A LEU* 1.3 76.9 - - - +
115A ASP* 1.3 49.7 + - - +
117A THR* 3.2 3.5 + - - -
118A CYS* 2.6 49.0 + - - +
12B GLU 5.7 2.0 - - - +
13B VAL* 5.1 4.0 - - + -
16B HIS* 4.3 27.4 - - + +
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Residues in contact with ASP 115 (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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111A LYS* 3.1 36.2 + - - +
112A ASN* 3.5 13.8 - - + +
114A LEU* 1.3 71.9 - - - +
116A LEU* 1.3 62.1 + - - +
118A CYS* 3.0 2.9 + - - +
119A GLN* 2.7 39.1 + - - +
16B HIS* 2.6 38.7 + - - -
20B PHE* 3.5 13.9 - - + -
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Residues in contact with LEU 116 (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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58A TYR* 4.4 16.6 - - + +
87A ASP* 3.4 35.2 - - - +
90A PHE* 4.6 5.6 - - + -
91A MET* 3.6 37.2 - - + -
112A ASN 3.1 15.3 + - - +
113A LEU* 3.3 6.5 + - + +
115A ASP* 1.3 79.5 - - - +
117A THR* 1.3 54.9 + - + +
119A GLN* 3.3 18.7 + - - +
120A THR* 2.6 35.3 + - - +
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Residues in contact with THR 117 (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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91A MET* 2.9 32.1 - - + -
98A LEU* 4.3 5.2 - - + +
101A LEU* 3.7 17.7 - - + -
102A ILE* 4.0 27.3 - - - +
105A ALA* 4.7 0.3 - - - +
113A LEU* 2.7 40.0 + - + +
114A LEU* 3.2 9.2 + - - -
116A LEU* 1.3 73.0 - - - +
118A CYS* 1.3 61.5 + - - +
120A THR* 3.3 7.6 + - - +
121A VAL* 3.1 33.1 + - - +
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Residues in contact with CYS 118 (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 ILE* 4.4 5.8 - - - -
114A LEU* 2.6 35.2 + - - +
115A ASP 3.0 1.5 + - - +
117A THR* 1.3 71.9 + - - +
119A GLN* 1.4 65.6 + - - +
120A THR 2.9 2.2 + - - -
121A VAL* 3.3 3.3 + - - +
122A ALA* 3.0 21.1 + - - +
13B VAL* 4.0 17.9 - - - -
16B HIS* 3.3 32.3 - - + +
17B VAL* 3.6 28.6 - - - +
20B PHE* 3.7 10.1 - - + -
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Residues in contact with GLN 119 (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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115A ASP* 2.7 22.0 + - - +
116A LEU* 3.3 35.5 + - - +
118A CYS* 1.4 70.3 - - - +
120A THR* 1.3 59.6 + - - +
122A ALA* 3.1 3.3 + - - +
123A ASP* 2.9 41.9 + - - +
20B PHE* 3.4 39.5 - - + -
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Residues in contact with THR 120 (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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91A MET* 4.1 22.8 - - + +
98A LEU* 4.0 25.8 - - + -
116A LEU* 2.6 23.3 + - - +
117A THR* 3.3 9.4 + - - -
118A CYS 2.9 1.6 - - - -
119A GLN* 1.3 79.1 - - - +
121A VAL* 1.3 62.2 + - - +
123A ASP* 3.4 14.1 + - - +
124A MET* 3.2 22.3 + - + +
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Residues in contact with VAL 121 (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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98A LEU* 3.8 20.2 - - + -
99A PHE* 4.8 7.0 - - + -
102A ILE* 3.4 25.1 - - + -
117A THR 3.1 15.6 + - - +
118A CYS 3.3 3.3 + - - +
120A THR* 1.3 75.1 - - - +
122A ALA* 1.3 66.7 + - - +
124A MET* 3.1 18.5 + - - +
125A ILE* 3.2 11.2 + - + +
137A PHE* 3.4 32.8 - - + -
9B PHE* 5.1 4.3 - - + -
17B VAL* 4.1 19.5 - - + -
37B TRP* 6.3 0.2 - - + -
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Residues in contact with ALA 122 (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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118A CYS 3.0 13.1 + - - +
119A GLN 3.1 9.4 - - - +
121A VAL* 1.3 75.6 - - - +
123A ASP* 1.3 60.0 + - - +
125A ILE* 2.5 34.6 + - - +
126A LYS* 3.2 10.6 - - + +
17B VAL* 4.0 9.5 - - - +
20B PHE* 3.8 22.9 - - + +
21B ILE* 3.8 23.1 - - + -
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Residues in contact with ASP 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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119A GLN* 2.9 31.5 + - - +
120A THR* 3.4 8.2 + - - +
121A VAL 3.2 0.8 - - - -
122A ALA* 1.3 74.4 - - - +
124A MET* 1.3 59.9 + - - +
126A LYS* 3.4 46.8 + - - +
20B PHE* 5.7 1.2 - - - +
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Residues in contact with MET 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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95A GLN* 5.0 21.1 - - + +
98A LEU* 4.3 25.4 - - + -
99A PHE* 5.4 3.8 - - - -
120A THR* 3.2 22.0 - - + +
121A VAL* 3.4 12.1 - - - +
122A ALA 2.8 0.6 + - - -
123A ASP* 1.3 77.1 - - - +
125A ILE* 1.3 67.6 + - + +
126A LYS 3.4 0.4 - - - -
128A LYS* 2.9 42.1 + - - +
136A THR* 4.9 1.9 + - - -
137A PHE* 4.8 14.5 - - + -
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Residues in contact with ILE 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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121A VAL* 3.4 18.8 - - + +
122A ALA* 2.5 20.6 + - - +
124A MET* 1.3 75.7 - - - +
126A LYS* 1.3 56.9 + - - +
128A LYS* 2.9 29.1 + - - +
133A ILE* 3.5 28.3 - - + -
137A PHE* 3.7 31.2 - - + -
17B VAL* 4.8 7.4 - - + -
18B PHE* 5.7 1.6 - - + -
21B ILE* 4.1 14.1 - - + -
26B ASP* 5.0 2.8 - - + +
29B SER* 6.0 0.2 - - - -
30B VAL* 3.6 26.0 - - + -
37B TRP* 4.5 16.4 - - + -
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Residues in contact with LYS 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 ALA* 3.2 17.2 + - + +
123A ASP* 3.4 39.7 + - - +
124A MET 3.4 2.0 - - - +
125A ILE* 1.3 73.9 - - - +
127A GLY* 1.3 59.1 + - - +
128A LYS* 3.0 16.9 + - - +
20B PHE* 4.6 13.1 + - - +
21B ILE* 4.0 19.7 - - + -
22B GLN 6.1 0.2 - - - +
26B ASP* 3.7 21.8 - - - +
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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