Contacts of the helix formed by residues 155 - 164 (chain A) in PDB entry 1H3F
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 ARG 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLN 3.9 1.4 + - - -
152A MET 3.1 15.0 + - - +
154A GLU* 1.3 76.0 - - - +
156A GLU* 1.3 73.9 + - + +
157A ASP* 4.2 20.3 + - - +
158A PHE* 3.0 36.2 + - + +
159A LYS 2.9 20.1 + - - -
172A GLU 5.2 0.8 + - - -
175A TYR* 6.0 0.4 - - - +
176A PRO* 3.4 18.6 - - - +
196A ASP 5.8 3.5 + - - -
197A GLN* 5.3 1.6 + - - -
199A PHE* 3.5 42.7 - - + -
200A ASN* 2.8 37.7 + - - +
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Residues in contact with GLU 156 (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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154A GLU 3.0 6.3 + - - -
155A ARG* 1.3 75.0 - - + +
157A ASP* 1.3 73.8 + - + +
159A LYS* 3.3 6.7 + - - +
160A LYS* 3.1 31.9 + - + +
195A THR 5.1 3.9 - - - +
196A ASP* 4.4 27.4 - - - +
199A PHE* 5.8 1.3 - - + +
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Residues in contact with ASP 157 (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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155A ARG* 3.4 18.6 + - - +
156A GLU* 1.3 88.4 - - + +
158A PHE* 1.3 66.4 + - - +
160A LYS* 3.6 6.2 + - - +
161A ARG* 3.1 57.1 + - - +
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Residues in contact with PHE 158 (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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152A MET* 3.3 36.1 - - + +
153A LEU* 4.3 11.2 - - + -
155A ARG* 3.0 45.5 + - + +
157A ASP* 1.3 78.6 - - - +
159A LYS* 1.3 54.5 + - - +
161A ARG* 3.1 26.5 + - - -
162A TYR* 2.7 38.0 + - - +
168A ILE* 3.5 35.1 - - + +
172A GLU* 3.9 27.1 - - + -
173A LEU* 4.0 21.1 - - + -
176A PRO* 5.1 0.2 - - + -
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Residues in contact with LYS 159 (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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153A LEU 3.5 20.1 + - - +
154A GLU* 4.2 20.6 - - - +
155A ARG 2.9 9.9 + - - +
156A GLU* 3.6 10.8 - - - +
158A PHE* 1.3 77.7 - - - +
160A LYS* 1.3 79.5 + - - +
162A TYR* 4.1 3.9 - - - +
163A GLU* 3.1 63.2 + - + +
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Residues in contact with LYS 160 (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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156A GLU* 3.1 18.9 + - + +
157A ASP* 4.0 5.4 - - - +
159A LYS* 1.3 105.0 - - - +
161A ARG* 1.3 65.0 + - + +
163A GLU* 3.7 14.7 + - - +
164A ALA* 3.1 25.6 + - - +
166A ILE* 5.6 0.2 - - - -
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Residues in contact with ARG 161 (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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157A ASP* 3.1 38.0 + - - +
158A PHE* 3.1 19.8 + - - +
160A LYS* 1.3 79.0 - - + +
162A TYR* 1.3 66.0 + - - +
164A ALA* 3.1 7.8 + - - -
166A ILE* 2.9 60.9 + - + +
167A PRO 3.1 20.2 + - - -
168A ILE* 3.8 17.6 - - + +
172A GLU* 2.5 40.2 + - - -
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Residues in contact with TYR 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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153A LEU* 4.2 23.8 - - + -
158A PHE 2.7 20.8 + - - +
159A LYS* 4.1 4.7 - - - +
161A ARG* 1.3 73.1 - - - +
163A GLU* 1.3 67.6 + - + +
165A GLY* 3.6 9.7 + - - -
166A ILE 4.5 3.4 - - - -
168A ILE* 4.0 12.5 - - + +
149B VAL* 4.5 4.5 - - + -
150B ALA* 4.1 31.8 - - + +
153B LEU* 3.4 31.2 - - + +
162B TYR* 4.0 26.5 - + - -
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Residues in contact with GLU 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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159A LYS* 3.1 52.0 + - + +
160A LYS* 3.7 14.2 + - - +
162A TYR* 1.3 83.1 - - + +
164A ALA* 1.3 58.3 + - - +
165A GLY 3.2 3.6 + - - -
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Residues in contact with ALA 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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160A LYS 3.1 18.9 + - - +
161A ARG 3.1 5.2 + - - +
163A GLU* 1.3 75.5 - - - +
165A GLY* 1.3 63.1 + - - +
166A ILE* 3.1 24.9 + - + +
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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