Contacts of the helix formed by residues 152 - 160 (chain I) in PDB entry 3GHG
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 152 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150I GLY 3.4 0.8 - - - -
151I LYS* 1.3 82.1 + - - +
153I CYS* 1.3 58.9 + - - +
154I GLN* 3.4 8.4 - - - +
155I ASP* 2.6 35.2 + - - +
156I ILE* 2.9 29.5 + - - +
169I ILE* 3.8 15.9 - - + -
192I THR* 4.8 6.1 - - - +
236I ILE* 4.9 7.2 - - + -
242I ILE* 5.7 0.2 - - - +
244I TYR* 3.1 31.3 + - + +
388I PRO* 3.5 22.5 - - - +
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Residues in contact with CYS 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152I ASP* 1.3 74.2 - - - +
154I GLN* 1.3 57.6 + - - +
156I ILE* 3.3 9.3 - - - +
157I ALA* 2.9 27.7 + - - +
169I ILE* 4.3 1.0 - - - +
180I VAL* 4.7 1.6 - - - -
182I CYS* 2.0 55.8 - - + -
184I ILE* 4.7 1.4 - - + +
190I GLY* 3.3 26.5 - - - +
192I THR* 2.8 40.1 + - - +
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Residues in contact with GLN 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152I ASP* 3.1 9.8 + - - +
153I CYS* 1.3 75.8 - - - +
155I ASP* 1.3 67.3 + - - +
157I ALA* 2.9 3.1 + - - +
158I ASN* 2.8 61.1 + - - +
188I GLY 3.3 8.1 + - - -
190I GLY* 2.7 32.8 + - - +
387I ILE* 4.1 4.2 - - - +
388I PRO* 3.7 30.1 - - + -
390I ASN* 5.9 1.6 - - - +
391I ARG* 3.0 41.6 - - + +
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Residues in contact with ASP 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I GLY* 4.5 0.4 - - - -
151I LYS* 3.5 40.2 + - + +
152I ASP* 2.6 23.4 + - - +
154I GLN* 1.3 71.8 - - - +
156I ILE* 1.3 66.8 + - - +
158I ASN* 3.4 11.7 + - - +
159I LYS* 3.0 56.6 + - - +
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Residues in contact with ILE 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I ILE* 4.6 10.1 - - + +
149I THR* 4.4 4.5 - - - -
150I GLY* 4.1 16.9 - - - +
152I ASP 2.9 16.1 + - - +
153I CYS* 3.3 19.1 - - - +
155I ASP* 1.3 73.4 - - - +
157I ALA* 1.3 56.6 + - - +
159I LYS* 2.7 33.0 + - - +
160I GLY 2.9 9.5 + - - -
161I ALA* 3.3 29.5 + - + -
167I TYR* 3.4 45.3 - - + -
168I PHE 4.4 2.9 - - - +
169I ILE* 4.2 10.1 - - + -
182I CYS* 4.1 5.8 - - + -
184I ILE* 4.4 4.0 - - + -
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Residues in contact with ALA 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153I CYS 2.9 18.3 + - - +
154I GLN* 2.9 10.4 + - - +
156I ILE* 1.3 74.3 - - - +
158I ASN* 1.3 59.2 + - - +
160I GLY* 2.9 23.0 + - - -
161I ALA 4.1 9.7 - - - +
184I ILE* 4.0 15.9 - - + -
188I GLY* 3.4 30.3 - - - +
190I GLY 4.5 3.8 - - - +
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Residues in contact with ASN 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I GLN* 2.8 54.7 + - - +
155I ASP* 3.8 12.1 + - - +
157I ALA* 1.3 71.9 - - - +
159I LYS* 1.3 61.4 + - - +
188I GLY 4.1 3.6 - - - +
391I ARG* 4.0 15.3 + - - +
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Residues in contact with LYS 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I ILE* 4.3 21.4 - - + +
149I THR 3.4 25.9 + - - +
150I GLY* 3.9 3.6 - - - -
155I ASP* 3.0 44.7 + - - +
156I ILE* 2.7 12.0 + - - +
158I ASN* 1.3 81.0 - - - +
160I GLY* 1.3 54.6 + - - +
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Residues in contact with GLY 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I ILE* 4.7 6.1 - - - +
156I ILE 2.9 5.7 + - - -
157I ALA 2.9 10.8 + - - -
159I LYS* 1.3 80.0 - - - +
161I ALA* 1.3 67.1 + - - +
162I LYS* 3.5 21.7 - - - +
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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