Contacts of the helix formed by residues 182 - 191 (chain A) in PDB entry 3H1S
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 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ASN 3.4 26.1 + - - +
80A CYS* 2.8 15.9 + - - +
81A LEU 4.2 1.2 + - - -
82A THR* 3.6 30.9 + - + -
86A THR* 3.5 6.1 - - - +
180A ILE 3.4 0.8 + - - -
181A VAL* 1.3 70.2 - - - +
183A TRP* 1.3 61.7 + - - +
184A GLN* 2.9 23.5 + - - +
185A PHE* 3.0 15.2 + - - +
186A VAL* 3.1 24.4 + - - +
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Residues in contact with TRP 183 (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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86A THR* 2.8 22.2 + - - +
87A GLU* 3.3 27.4 - - - -
88A ALA* 4.1 19.2 - - + -
92A LEU* 4.1 13.0 - - + +
96A LEU* 4.3 20.4 - - + -
103A VAL* 5.3 6.1 - - + -
106A PHE* 3.9 29.2 - + - -
107A LYS* 4.5 13.6 - - + +
125A LEU* 5.7 1.3 - - + -
153A LEU* 4.9 2.9 - - + -
178A TRP* 3.7 29.0 + + - -
181A VAL* 3.1 38.6 + - + +
182A ASN* 1.3 70.0 - - - +
184A GLN* 1.3 55.9 + - - +
186A VAL* 3.9 16.7 - - + +
187A SER* 2.7 36.9 + - - -
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Residues in contact with GLN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 3.8 14.6 - - + +
87A GLU 4.1 14.5 + - - +
89A SER 6.0 0.2 - - - +
182A ASN* 2.9 11.1 + - - +
183A TRP* 1.3 74.1 - - - +
185A PHE* 1.3 60.7 + - - +
187A SER* 3.2 10.4 + - - -
188A GLU* 2.8 55.4 + - - +
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Residues in contact with PHE 185 (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 PHE* 3.7 36.3 - + - -
79A ASN* 3.4 60.3 - - + +
80A CYS* 3.8 16.6 - - - -
152A LEU 4.3 1.3 - - - -
182A ASN* 3.0 19.0 + - - +
184A GLN* 1.3 76.5 - - - +
186A VAL* 1.3 66.3 + - + +
188A GLU* 3.2 15.4 + - - +
189A GLN* 3.0 63.4 + - + +
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Residues in contact with VAL 186 (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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80A CYS* 5.3 0.7 - - + -
92A LEU* 3.6 20.2 - - + -
125A LEU* 4.4 13.9 - - + -
152A LEU* 3.6 37.6 - - + +
153A LEU* 3.8 26.5 - - + -
181A VAL* 4.4 1.8 - - + -
182A ASN 3.1 19.1 + - - +
183A TRP* 4.0 19.5 - - + +
184A GLN 3.3 0.2 - - - -
185A PHE* 1.3 77.3 - - + +
187A SER* 1.3 56.4 + - - +
189A GLN* 3.7 2.8 + - - +
190A PHE* 3.1 28.9 + - - +
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Residues in contact with SER 187 (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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87A GLU 4.0 1.1 + - - -
88A ALA* 3.7 0.3 - - - -
89A SER* 3.0 44.3 + - - -
91A GLN* 5.3 2.3 + - - -
92A LEU* 3.5 12.4 - - - +
183A TRP 2.7 22.2 + - - -
184A GLN* 3.5 13.9 - - - -
185A PHE 3.2 0.2 - - - -
186A VAL* 1.3 75.5 - - - +
188A GLU* 1.3 64.6 + - - +
190A PHE* 3.3 6.2 + - - +
191A ALA* 3.1 20.3 + - - +
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A GLN* 2.8 45.0 + - - +
185A PHE* 3.8 20.0 - - - +
187A SER* 1.3 71.3 - - - +
189A GLN* 1.3 69.9 + - - +
191A ALA* 2.9 24.3 + - - +
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Residues in contact with GLN 189 (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 PHE* 4.1 17.5 - - + -
150A LYS* 5.7 4.3 - - - +
151A PRO 3.8 15.8 + - - +
152A LEU* 3.8 13.3 - - + +
185A PHE* 3.0 62.1 + - + +
186A VAL 3.8 4.5 - - - +
188A GLU* 1.3 79.5 - - - +
190A PHE* 1.3 62.8 + - - +
191A ALA 3.3 2.9 + - - -
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Residues in contact with PHE 190 (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 GLN* 3.6 51.8 - - + -
92A LEU* 3.9 19.7 - - + -
95A ALA* 4.1 14.6 - - + -
127A LYS* 3.7 40.5 + - - +
133A LEU* 4.1 11.2 - - + -
152A LEU* 3.7 30.7 - - + -
186A VAL 3.1 19.2 + - - +
187A SER* 3.6 7.6 - - - +
188A GLU 3.1 0.4 - - - -
189A GLN* 1.3 76.1 - - - +
191A ALA* 1.3 73.4 - - - +
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Residues in contact with ALA 191 (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 GLN* 4.7 17.1 - - - +
127A LYS* 4.5 6.4 + - - -
187A SER 3.1 10.7 + - - +
188A GLU* 2.9 20.4 + - - +
189A GLN 3.2 2.9 - - - -
190A PHE* 1.3 88.1 - - - +
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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