Contacts of the helix formed by residues 157 - 173 (chain A) in PDB entry 2FOL
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 ASN 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A LEU* 3.8 15.3 - - + +
149A GLU* 2.8 31.1 + - - +
150A THR* 3.9 5.2 - - + -
155A ALA 4.1 1.4 + - - -
156A THR* 1.3 80.8 - - - +
158A VAL* 1.3 57.1 + - - +
159A GLU 3.2 2.7 - - - -
160A GLN* 2.7 36.8 + - - +
161A SER* 2.8 32.4 + - - -
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.6 29.6 - - + +
27A ARG* 3.8 25.6 - - + -
28A PHE* 3.6 30.7 - - + -
150A THR* 4.7 1.6 - - - -
151A SER 3.6 25.1 - - - +
152A ALA* 4.1 0.4 - - - -
155A ALA* 4.4 3.2 + - - -
156A THR 3.0 11.0 - - - +
157A ASN* 1.3 78.6 - - - +
159A GLU* 1.3 62.5 + - + +
161A SER* 3.4 10.0 - - - -
162A PHE* 3.1 24.1 - - + -
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Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.2 27.0 - - + +
48A ARG* 3.0 40.5 + - - +
158A VAL* 1.3 77.9 - - - +
160A GLN* 1.3 66.5 + - - +
161A SER 3.0 1.7 + - - -
162A PHE* 3.3 0.9 + - - +
163A MET* 2.8 41.9 + - + +
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Residues in contact with GLN 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 3.7 13.4 - - + +
157A ASN* 2.7 43.9 + - - +
159A GLU* 1.3 77.5 - - - +
161A SER* 1.3 50.0 + - - +
163A MET* 3.3 7.2 - - - +
164A THR* 2.7 43.7 + - - +
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Residues in contact with SER 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 6.4 0.4 - - - -
85A ILE* 5.2 2.9 - - - -
117A LEU* 3.2 27.1 - - - +
119A VAL* 4.3 6.1 - - - +
148A LEU* 3.9 15.6 - - - +
150A THR* 3.1 23.8 - - - +
157A ASN 2.8 15.9 + - - -
158A VAL* 3.4 11.9 - - - -
159A GLU 3.0 0.4 - - - -
160A GLN* 1.3 77.4 - - - +
162A PHE* 1.3 63.3 + - - +
164A THR* 3.5 1.5 + - - -
165A MET* 3.0 21.1 + - - +
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Residues in contact with PHE 162 (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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11A LEU* 3.8 23.2 - - + +
13A LEU* 4.2 18.8 - - + -
24A LEU* 4.5 9.2 - - + -
25A LEU* 4.6 14.1 - - - -
28A PHE* 3.3 64.4 - + + -
50A ILE* 5.5 0.9 - - - -
59A LEU* 4.6 7.7 - - + +
61A ILE* 4.3 15.3 - - + -
85A ILE* 3.7 20.6 - - + -
158A VAL* 3.1 28.0 - - + -
159A GLU 3.3 2.0 + - - +
161A SER* 1.3 80.9 - - - +
163A MET* 1.3 60.6 - - - +
165A MET* 3.1 6.6 + - - +
166A ALA* 2.8 29.5 + - - +
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Residues in contact with MET 163 (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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28A PHE* 5.9 0.4 - - + -
50A ILE* 4.3 28.0 - - + -
51A GLU 4.3 10.1 - - - +
52A LEU* 3.6 28.3 - - + +
159A GLU* 2.8 41.3 + - + +
160A GLN* 3.3 7.4 - - - +
162A PHE* 1.3 77.5 - - - +
164A THR* 1.3 56.7 + - - +
166A ALA* 3.5 7.0 + - - +
167A ALA* 2.9 29.2 + - - +
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Residues in contact with THR 164 (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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117A LEU* 4.4 2.7 - - + -
146A PRO* 4.0 23.6 - - + -
148A LEU* 3.6 28.6 - - + +
160A GLN* 2.7 30.9 + - - +
161A SER 3.6 6.1 - - - -
162A PHE 3.3 0.2 - - - -
163A MET* 1.3 72.6 - - - +
165A MET* 1.3 58.2 + - - +
167A ALA* 3.3 8.8 - - + +
168A GLU* 3.0 31.6 + - - +
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Residues in contact with MET 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.9 26.0 - - + -
83A GLY* 3.7 13.9 - - - -
84A ILE 3.1 44.0 - - - +
85A ILE* 3.8 14.4 - - + -
115A ASN* 3.7 18.6 - - - +
116A LYS 3.9 1.6 - - - -
117A LEU* 3.8 22.0 - - + +
146A PRO* 6.4 0.4 - - - -
161A SER 3.0 14.5 + - - +
162A PHE* 3.1 11.4 + - - +
164A THR* 1.3 73.3 - - - +
166A ALA* 1.3 67.5 + - - +
168A GLU* 3.0 15.4 + - - -
169A ILE* 3.0 22.4 + - + +
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Residues in contact with ALA 166 (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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9A PHE* 3.9 22.2 - - + -
11A LEU* 5.5 1.0 - - - +
50A ILE* 4.0 17.9 - - + -
52A LEU* 3.4 23.6 - - + -
57A ILE* 4.6 2.0 - - + -
59A LEU* 4.8 6.3 - - + -
162A PHE 2.8 15.3 + - - +
163A MET 3.6 4.9 - - - +
165A MET* 1.3 70.5 - - - +
167A ALA* 1.3 65.1 + - - +
169A ILE* 2.9 5.3 + - - +
170A LYS* 2.8 26.1 + - - +
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Residues in contact with ALA 167 (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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52A LEU* 3.8 14.9 - - + +
53A ASP* 6.2 0.4 - - - +
163A MET 2.9 15.6 + - - +
164A THR* 3.3 15.5 - - + +
166A ALA* 1.3 74.8 - - - +
168A GLU* 1.3 61.1 + - - +
170A LYS* 3.6 4.9 + - - +
171A LYS* 3.0 28.5 + - - +
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Residues in contact with GLU 168 (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 ASN* 3.4 33.5 + - + +
116A LYS 5.3 1.8 - - - +
146A PRO* 3.9 31.4 - - + +
164A THR* 3.0 18.9 + - - +
165A MET* 3.0 12.4 + - - +
167A ALA* 1.3 79.0 - - - +
169A ILE* 1.3 61.9 + - - +
171A LYS* 3.3 49.4 + - - +
172A ARG* 3.3 6.9 + - - +
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Residues in contact with ILE 169 (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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9A PHE* 3.8 20.9 - - + -
11A LEU* 3.8 22.4 - - + -
82A HIS* 3.4 28.9 - - + +
83A GLY 3.8 9.0 - - - +
115A ASN* 3.2 24.0 - - + +
165A MET* 3.0 20.8 + - + +
166A ALA* 2.9 5.9 + - - +
168A GLU* 1.3 73.8 - - - +
170A LYS* 1.3 65.7 + - - +
171A LYS 3.0 1.6 - - - -
172A ARG* 3.1 15.1 + - - +
173A MET* 3.2 47.6 - - + +
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Residues in contact with LYS 170 (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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7A TYR* 4.1 26.6 + - + +
9A PHE* 3.9 14.8 - - + -
52A LEU* 4.4 9.6 - - + -
53A ASP* 3.8 23.9 + - - +
55A LYS* 3.5 42.6 - - - +
57A ILE* 4.4 13.0 - - + -
166A ALA 2.8 19.2 + - - +
167A ALA* 3.9 5.2 - - - +
169A ILE* 1.3 74.0 - - - +
171A LYS* 1.3 61.2 + - - +
173A MET* 3.4 19.9 + - - +
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Residues in contact with LYS 171 (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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167A ALA 3.0 18.2 + - - +
168A GLU* 3.3 32.0 + - - +
169A ILE 3.0 0.2 - - - -
170A LYS* 1.3 77.1 - - - +
172A ARG* 1.3 60.2 + - - +
173A MET 3.1 9.7 + - - +
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Residues in contact with ARG 172 (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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82A HIS* 3.1 23.2 + - - +
111A SER* 5.3 6.5 - - - -
113A ASN* 3.1 44.4 + - + +
114A VAL* 4.1 3.0 - - - +
115A ASN* 2.7 44.5 + - - +
168A GLU 3.3 3.0 + - - +
169A ILE* 3.1 16.3 + - - +
171A LYS* 1.3 76.7 - - - +
173A MET* 1.3 70.0 + - + +
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Residues in contact with MET 173 (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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7A TYR* 4.7 20.4 - - + +
9A PHE* 3.6 22.7 - - + -
82A HIS* 3.1 36.3 - - + +
169A ILE* 3.2 28.2 + - + +
170A LYS* 3.7 15.8 - - - +
171A LYS 3.1 10.1 - - - +
172A ARG* 1.3 94.9 - - + +
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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