Contacts of the helix formed by residues 169 - 181 (chain A) in PDB entry 2HEI
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 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A MET* 4.2 17.4 - - - +
161A GLU* 2.8 29.6 + - - +
162A THR* 4.1 4.2 - - + +
167A ALA 3.0 2.4 + - - -
168A MET* 1.3 90.6 - - - +
170A VAL* 1.3 58.6 + - - +
171A ASN 3.6 1.6 - - - -
172A ASP* 3.4 20.3 + - - +
173A LEU* 2.9 29.8 + - - +
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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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36A LEU* 3.6 46.9 - - + +
39A ARG* 4.0 15.5 - - + -
40A PHE* 4.1 14.4 - - + +
162A THR* 4.5 6.1 - - - -
163A SER 3.6 19.7 - - - +
164A ALA* 4.1 4.0 - - - +
167A ALA* 3.0 20.5 + - + +
168A MET 3.9 3.6 - - - +
169A ASN* 1.3 73.4 - - - +
171A ASN* 1.3 68.7 + - - +
173A LEU* 3.1 12.5 + - - +
174A PHE* 3.3 22.4 + - + -
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Residues in contact with ASN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 4.6 4.2 - - - +
40A PHE* 3.4 41.1 - - + +
62A VAL* 4.9 2.4 - - + +
167A ALA* 4.6 3.4 + - - -
170A VAL* 1.3 78.3 - - - +
172A ASP* 1.3 64.1 + - - +
174A PHE* 3.2 4.9 + - - +
175A LEU* 3.0 26.5 + - - +
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Residues in contact with ASP 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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160A MET* 3.3 20.9 - - + +
169A ASN* 3.4 23.5 + - + +
170A VAL 3.1 1.2 - - - -
171A ASN* 1.3 80.4 - - - +
173A LEU* 1.3 63.8 + - - +
175A LEU* 3.6 19.0 - - + +
176A ALA* 3.0 18.5 + - - +
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Residues in contact with LEU 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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36A LEU* 6.2 1.3 - - + -
97A ILE* 4.2 19.7 - - + -
129A ALA* 4.0 19.5 - - + -
130A LEU 4.8 0.4 - - - +
131A ALA* 3.6 32.8 - - + -
158A LEU* 4.9 8.3 - - + -
160A MET* 3.7 34.1 - - + +
162A THR* 4.1 12.8 - - + -
169A ASN 2.9 17.3 + - - +
170A VAL 3.1 6.0 + - - +
172A ASP* 1.3 77.7 - - - +
174A PHE* 1.3 63.9 + - + +
176A ALA* 3.2 2.8 + - + +
177A ILE* 3.1 34.9 + - + +
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Residues in contact with PHE 174 (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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23A LEU* 4.0 19.5 - - + -
25A LEU* 4.7 10.3 - - + -
36A LEU* 4.6 9.9 - - + -
37A VAL* 5.1 3.1 - - - -
40A PHE* 3.6 58.6 - + + -
62A VAL* 4.3 1.3 - - + -
71A PHE* 3.5 21.6 - + + -
73A ILE* 3.8 22.9 - - + -
97A ILE* 3.7 28.3 - - + -
170A VAL* 3.3 28.5 - - + -
171A ASN 3.2 6.3 + - - +
173A LEU* 1.3 82.1 - - + +
175A LEU* 1.3 55.6 + - - +
177A ILE* 3.4 5.0 + - + -
178A ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 175 (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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62A VAL* 3.3 32.8 - - + +
63A CYS 4.3 4.5 - - - +
64A LEU* 3.4 25.6 - - + -
171A ASN 3.0 13.4 + - - +
172A ASP* 3.6 23.1 - - + +
173A LEU 3.2 0.2 - - - -
174A PHE* 1.3 74.3 - - - +
176A ALA* 1.3 65.0 + - - +
178A ALA* 3.1 3.5 + - - +
179A LYS* 3.0 43.2 + - - +
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Residues in contact with ALA 176 (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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158A LEU* 3.7 19.4 - - + +
160A MET* 3.7 17.9 - - + -
172A ASP 3.0 17.4 + - - +
173A LEU* 3.2 7.2 + - + +
175A LEU* 1.3 75.7 - - - +
177A ILE* 1.3 63.1 + - - +
179A LYS* 3.4 12.0 + - - +
180A LYS* 3.4 24.4 + - - +
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Residues in contact with ILE 177 (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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23A LEU* 4.1 7.4 - - + -
71A PHE* 4.2 7.0 - - + -
95A ALA* 3.7 27.8 - - + -
96A ALA 5.0 2.0 - - - +
97A ILE* 3.6 36.3 - - + -
127A VAL* 4.2 9.9 - - + +
129A ALA* 3.8 14.6 - - + +
158A LEU* 3.7 20.4 - - + -
173A LEU* 3.1 19.3 + - + +
174A PHE* 3.6 8.7 - - - +
175A LEU 3.2 0.2 - - - -
176A ALA* 1.3 75.9 - - - +
178A ALA* 1.3 64.5 + - - +
180A LYS* 3.0 13.6 + - - +
181A LEU* 3.1 22.2 + - + +
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Residues in contact with ALA 178 (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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62A VAL* 4.6 4.7 - - + -
64A LEU* 3.9 18.8 - - + +
69A VAL* 3.9 25.7 - - + +
71A PHE* 3.9 17.0 - - + -
174A PHE 2.9 14.7 + - - +
175A LEU* 3.1 13.0 + - - +
177A ILE* 1.3 77.7 - - - +
179A LYS* 1.3 61.0 + - - +
181A LEU* 3.3 23.0 + - - +
183A LYS* 4.7 1.4 + - - -
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Residues in contact with LYS 179 (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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64A LEU* 3.4 35.1 - - + +
175A LEU* 3.0 38.4 + - + +
176A ALA* 3.7 11.7 - - - +
177A ILE 3.2 0.2 - - - -
178A ALA* 1.3 75.5 - - - +
180A LYS* 1.3 61.4 + - + +
181A LEU 3.7 2.3 + - - +
183A LYS* 3.9 15.8 + - - +
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Residues in contact with LYS 180 (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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127A VAL* 4.0 26.2 - - + +
158A LEU* 4.0 25.1 - - + -
176A ALA 3.4 12.5 + - - +
177A ILE 3.0 9.4 + - - +
179A LYS* 1.3 75.6 - - + +
181A LEU* 1.3 65.3 + - - +
182A PRO* 4.8 0.3 - - - +
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Residues in contact with LEU 181 (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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21A PHE* 3.7 28.7 - - + -
71A PHE* 3.7 29.4 - - + -
94A GLN* 3.5 36.8 - - + +
95A ALA* 4.6 2.7 - - + -
125A SER 5.8 0.4 - - - +
127A VAL* 3.8 14.8 - - + -
177A ILE* 3.1 21.2 + - + +
178A ALA* 3.3 15.6 + - - +
179A LYS 3.9 6.6 - - - +
180A LYS* 1.3 83.3 - - - +
182A PRO* 1.4 81.1 - - + +
183A LYS* 3.9 7.8 + - - +
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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