Contacts of the helix formed by residues 136 - 141 (chain A) in PDB entry 3HIG
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 SER 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A TYR* 3.4 27.6 + - - -
135A GLN* 1.3 79.3 + - - +
137A SER* 1.3 64.4 + - - +
138A TRP 3.2 3.5 + - - -
139A ALA* 3.2 5.7 + - - +
140A SER 3.0 17.2 + - - -
194A SER* 3.2 23.4 + - - -
195A GLY* 3.2 24.5 - - - -
642A ASP* 3.8 2.0 - - - -
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Residues in contact with SER 137 (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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110A ASN* 3.3 13.5 - - - +
111A VAL* 3.1 42.7 + - - +
134A TYR* 3.4 20.5 + - - -
135A GLN 3.5 3.6 + - - -
136A SER* 1.3 77.0 - - - +
138A TRP* 1.3 63.1 + - - +
140A SER* 2.8 25.5 + - - -
141A ARG 3.4 4.0 + - - -
638A TYR* 6.1 1.1 - - - -
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Residues in contact with TRP 138 (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 MET* 3.6 20.6 - - - -
66A LYS 4.5 1.1 - - - -
102A PHE* 3.9 14.6 - + + -
103A PHE 3.7 4.7 - - - -
104A GLY* 3.3 30.1 - - - -
109A PRO* 3.4 37.6 + - + +
110A ASN* 3.5 28.0 - - - +
111A VAL* 4.4 1.1 - - + -
135A GLN 5.2 0.6 + - - -
136A SER 3.2 1.0 - - - -
137A SER* 1.3 80.6 + - - +
139A ALA* 1.3 64.7 + - - +
141A ARG* 2.9 86.5 + - - +
224A GLY 4.3 14.7 + - - -
226A THR* 3.5 18.0 - - + +
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Residues in contact with ALA 139 (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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136A SER* 3.2 7.2 + - - +
138A TRP* 1.3 80.8 - - - +
140A SER* 1.3 58.1 + - - +
141A ARG* 3.2 1.6 - - - +
195A GLY* 3.3 45.3 - - - +
196A GLN 4.1 11.6 - - - +
197A ARG* 2.9 28.8 + - + +
641A ASN* 3.7 12.6 - - - +
642A ASP* 5.7 0.4 - - + -
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 3.7 17.3 - - - -
136A SER 3.0 12.9 + - - -
137A SER* 2.8 21.0 + - - -
139A ALA* 1.3 75.1 - - - +
141A ARG* 1.3 62.8 + - - +
142A PRO* 3.8 0.7 - - - +
637A ILE 4.3 0.7 - - - +
638A TYR* 3.5 44.3 - - - +
641A ASN* 3.4 21.9 - - - +
642A ASP* 3.9 11.4 - - - +
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Residues in contact with ARG 141 (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 MET* 3.5 31.5 - - - +
102A PHE* 3.6 24.9 - - + -
111A VAL* 3.7 18.6 - - + -
137A SER 3.4 0.6 + - - -
138A TRP* 2.9 80.0 + - - +
139A ALA 3.2 3.0 - - - -
140A SER* 1.3 79.0 + - - +
142A PRO* 1.3 74.1 + - + +
147A GLU* 3.8 13.9 + - - -
197A ARG* 2.9 35.0 + - - +
223A HIS 5.4 2.0 + - - -
224A GLY 5.3 1.6 + - - -
638A TYR* 4.6 2.9 - - - -
641A ASN* 2.6 24.5 + - - -
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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