Contacts of the helix formed by residues 162 - 172 (chain A) in PDB entry 5EN1
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 ASP 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ARG* 2.7 43.6 + - - -
112A LYS* 3.7 13.8 - - - +
160A PHE* 3.2 10.6 - - - +
161A ASP* 1.3 93.4 + - - +
163A HIS* 1.3 70.4 + - - +
164A ASP* 3.1 19.3 + - - +
165A PRO* 3.3 22.0 - - + +
166A VAL* 4.5 1.4 + - - +
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Residues in contact with HIS 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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79A MET* 4.4 6.1 - - + -
82A ARG* 3.3 26.5 + - - -
92A GLU* 5.8 4.8 + - - +
93A PRO 4.0 9.4 + - - -
94A LYS* 4.0 24.9 - - + +
110A THR* 3.4 32.9 + - + +
111A VAL 3.5 24.5 - - - +
112A LYS* 3.8 6.8 - - + +
162A ASP* 1.3 80.1 - - - +
164A ASP* 1.3 71.2 + - - +
166A VAL* 3.2 8.8 + - - +
167A ASP* 2.9 46.2 + - - +
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Residues in contact with ASP 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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79A MET* 3.5 34.1 - - + +
82A ARG* 3.6 9.4 + - - +
95A ARG* 2.8 46.7 + - - +
162A ASP* 3.1 18.0 + - - +
163A HIS* 1.3 79.5 - - + +
165A PRO* 1.4 61.0 - - + +
167A ASP* 3.0 7.0 + - - +
168A LYS* 2.7 34.7 + - - +
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Residues in contact with PRO 165 (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 ARG* 5.4 0.4 - - - +
135A TYR* 3.5 31.4 - - + +
136A GLY* 4.7 4.0 - - - -
160A PHE* 3.8 32.8 - - + -
161A ASP* 5.4 1.6 - - - +
162A ASP* 3.3 28.5 - - + +
164A ASP* 1.4 92.7 - - + +
166A VAL* 1.3 54.8 + - - +
168A LYS* 3.8 6.6 - - + +
169A ILE* 2.8 37.4 + - + +
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Residues in contact with VAL 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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111A VAL 3.8 10.3 - - - +
112A LYS* 3.4 34.1 - - - +
113A LYS 4.6 2.7 - - - +
114A LEU* 3.9 25.8 - - + +
160A PHE* 3.8 14.8 - - + -
162A ASP 4.5 1.8 - - - +
163A HIS 3.2 9.1 + - - +
164A ASP 3.1 1.0 - - - -
165A PRO* 1.3 76.7 - - - +
167A ASP* 1.3 62.0 + - - +
169A ILE* 3.1 7.1 + - - +
170A VAL* 2.9 35.5 + - + +
186A LYS* 3.9 30.1 - - + -
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Residues in contact with ASP 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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94A LYS* 5.0 2.9 - - - +
95A ARG* 4.1 29.9 + - + -
110A THR* 5.2 4.7 + - - -
111A VAL 4.9 4.3 + - - +
163A HIS* 2.9 39.3 + - - +
164A ASP* 3.0 7.4 + - - +
166A VAL* 1.3 83.6 - - - +
168A LYS* 1.3 63.9 + - - +
170A VAL* 3.4 4.1 + - - +
171A LEU* 3.0 27.9 + - + +
186A LYS* 4.4 13.6 - - - +
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Residues in contact with LYS 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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72A MET* 5.6 5.8 - - - +
76A ASP* 3.4 38.0 + - - +
95A ARG* 3.8 26.1 - - - +
134A GLU 5.7 2.4 + - - -
135A TYR* 3.8 24.9 - - + +
164A ASP* 2.7 20.9 + - - +
165A PRO* 3.8 6.5 - - + +
167A ASP* 1.3 72.9 - - - +
169A ILE* 1.3 64.4 + - - +
171A LEU* 3.5 6.1 + - - +
172A GLN* 3.3 45.6 + - + +
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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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114A LEU* 3.9 25.4 - - + -
132A PHE* 3.6 20.4 - - + -
135A TYR* 3.7 31.0 - - + -
160A PHE* 3.5 35.4 - - + -
165A PRO 2.8 26.6 + - - +
166A VAL* 3.5 4.3 - - - +
168A LYS* 1.3 75.0 - - - +
170A VAL* 1.3 54.6 + - - +
172A GLN* 2.3 35.8 - - - +
175A HIS* 2.7 26.2 + - + +
184A VAL* 4.0 9.0 - - + -
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Residues in contact with VAL 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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114A LEU* 3.7 22.9 - - + -
166A VAL* 2.9 26.6 + - + +
167A ASP* 4.1 4.3 - - - +
169A ILE* 1.3 75.5 - - - +
171A LEU* 1.3 62.1 + - - +
172A GLN 3.5 0.8 + - - -
173A LYS* 3.6 20.0 - - + +
184A VAL* 3.7 24.7 - - - +
185A ARG* 3.9 17.0 - - + -
186A LYS* 4.2 9.0 - - + +
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Residues in contact with LEU 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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19A GLN* 4.2 21.1 - - + +
20A PHE* 3.4 65.4 - - + +
72A MET* 4.5 9.9 - - - -
95A ARG* 4.6 26.5 - - + +
96A ALA 4.5 13.7 - - - +
167A ASP 3.0 17.1 + - - +
168A LYS* 3.5 7.4 - - - +
170A VAL* 1.3 74.9 - - - +
172A GLN* 1.3 61.3 + - + +
173A LYS* 3.5 3.8 + - - +
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Residues in contact with GLN 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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20A PHE* 5.6 0.4 - - + -
72A MET* 4.8 20.6 - - + +
135A TYR* 2.8 33.2 + - - -
168A LYS* 3.3 37.6 + - + +
169A ILE 2.3 25.6 + - - +
170A VAL 3.7 0.2 - - - -
171A LEU* 1.3 72.0 - - + +
173A LYS* 1.3 56.7 + - - +
174A TYR* 3.3 7.9 - - - +
175A HIS* 2.5 25.0 + - + +
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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