Contacts of the helix formed by residues 116 - 121 (chain A) in PDB entry 4H1S
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 GLY 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLY* 3.9 0.4 - - - -
85A ASP* 3.6 5.2 - - - -
114A ALA 3.6 2.2 + - - -
115A LEU* 1.3 74.3 - - - +
117A ASN* 1.3 66.6 + - - +
118A HIS 3.2 3.1 - - - -
119A GLU* 2.7 32.2 + - - +
120A PHE* 3.5 9.0 - - - -
177A THR* 4.0 4.5 - - - -
220A HIS* 3.5 23.8 - - - -
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Residues in contact with ASN 117 (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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85A ASP* 3.4 0.4 + - - -
116A GLY* 1.3 72.0 - - - -
118A HIS* 1.3 77.0 + - - +
120A PHE* 3.1 13.0 + - - +
177A THR* 4.3 2.0 - - - +
178A SER* 5.1 2.1 - - - -
181A THR* 3.6 31.0 - - + +
184A LEU* 3.8 37.5 + - + +
185A SER* 3.0 24.5 + - - -
220A HIS* 3.1 7.7 + - - -
243A HIS* 3.2 3.5 + - - -
602A ZN 2.3 28.5 - - - -
604A PO4 2.8 19.8 + - - -
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Residues in contact with HIS 118 (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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38A HIS* 3.5 7.2 - + - -
85A ASP* 2.9 22.6 + - - +
87A TYR* 3.3 31.4 - - + +
88A GLN* 4.3 3.4 - - + +
117A ASN* 1.3 94.8 + - - +
119A GLU* 1.3 60.2 + - - +
120A PHE 3.0 6.9 + - - -
121A ASP* 2.7 45.3 + - - +
184A LEU 5.1 6.7 - - - -
395A ARG* 3.3 8.0 + - - -
417A PHE* 3.6 31.2 - + - -
604A PO4 2.6 36.9 + - - -
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Residues in contact with GLU 119 (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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84A GLY* 3.7 1.4 - - - -
85A ASP* 2.8 15.8 + - - -
86A GLN* 2.8 26.5 + - - +
87A TYR* 2.9 33.6 + - + -
113A MET* 3.5 19.5 - - + +
115A LEU* 4.0 16.8 - - + -
116A GLY* 2.7 38.4 + - - +
117A ASN 3.2 1.0 - - - -
118A HIS* 1.3 76.2 - - - +
120A PHE* 1.3 60.4 + - + +
121A ASP 3.4 0.4 - - - -
122A ASN 5.0 0.2 + - - -
123A GLY 4.5 1.0 - - - +
127A LEU* 3.5 32.7 - - + +
131A LEU* 4.1 13.9 - - + -
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Residues in contact with PHE 120 (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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115A LEU* 4.0 13.9 - - + -
116A GLY 3.5 20.2 - - - -
117A ASN 3.1 5.1 + - - +
118A HIS 3.0 1.6 - - - -
119A GLU* 1.3 77.3 - - + +
121A ASP* 1.3 63.3 + - - +
122A ASN 3.2 3.1 - - - -
123A GLY 3.1 15.6 + - - -
124A VAL* 4.6 9.4 - - + -
127A LEU* 3.6 28.0 - - + -
144A ILE* 3.6 33.0 - - + -
177A THR* 4.5 2.5 - - + -
181A THR* 3.9 8.7 - - + -
185A SER* 2.9 17.5 + - - +
186A ASN 3.1 12.8 + - - +
187A PRO* 3.7 28.5 - - + -
191A LEU* 3.5 24.5 - - + -
193A PHE* 4.2 7.4 - + - -
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Residues in contact with ASP 121 (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 TYR* 5.3 2.2 - - + -
88A GLN* 3.0 33.0 + - - +
93A PHE* 5.3 0.4 - - + -
118A HIS* 2.7 49.6 + - - +
119A GLU 3.4 0.8 - - - -
120A PHE* 1.3 77.9 - - - +
122A ASN* 1.3 64.2 + - - +
123A GLY 3.3 1.0 + - - -
184A LEU 4.5 1.2 - - - +
185A SER* 2.5 35.4 + - - -
186A ASN* 2.9 25.1 + - - +
417A PHE* 3.5 9.5 - - + -
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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