Contacts of the helix formed by residues 113 - 121 (chain A) in PDB entry 3HVH
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ALA 3.0 12.1 + - - -
112A CYS* 1.3 77.7 - - - +
114A TYR* 1.3 65.3 + - - +
115A SER 3.4 2.5 - - - -
116A ALA* 3.2 6.8 + - - +
117A VAL* 2.9 31.2 + - - +
142A THR* 3.1 26.1 + - - -
145A MET* 4.7 4.9 - - - -
146A LEU* 5.8 0.4 - - - -
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Residues in contact with TYR 114 (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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69A LEU* 3.6 31.0 - - + +
72A ILE* 3.7 31.5 - - + +
73A ASP* 2.7 43.4 + - - -
84A ASN* 3.7 26.9 - - + +
85A VAL* 3.4 33.4 - - + -
86A GLY* 3.3 19.3 - - - -
110A ALA 4.4 1.4 + - - -
112A CYS* 3.5 3.0 + - + +
113A GLY* 1.3 78.8 - - - +
115A SER* 1.3 57.6 + - - +
117A VAL* 3.3 1.2 + - - -
118A ARG* 3.0 57.4 + - - +
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Residues in contact with SER 115 (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 VAL* 4.1 12.1 - - - +
93A MET* 4.0 11.4 - - - -
107A GLU* 2.6 23.7 + - - -
109A GLY 4.9 1.2 + - - -
110A ALA 4.7 4.5 + - - -
113A GLY 3.4 0.2 - - - -
114A TYR* 1.3 79.2 - - - +
116A ALA* 1.3 58.2 + - - +
118A ARG* 3.5 7.3 - - - +
119A MET* 2.9 37.7 + - - +
182A PHE* 3.9 24.1 - - - -
184A ASP* 4.5 5.4 + - - -
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Residues in contact with ALA 116 (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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107A GLU* 3.4 21.5 + - - +
110A ALA* 5.5 0.4 - - + -
113A GLY* 3.2 15.7 + - - +
115A SER* 1.3 77.5 + - - +
117A VAL* 1.3 60.0 + - - +
120A ALA* 2.9 34.3 + - - +
129A LEU* 3.7 16.7 - - + +
131A THR* 4.6 3.1 - - + -
142A THR* 4.6 5.8 - - + -
146A LEU* 4.0 23.6 - - + -
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Residues in contact with VAL 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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65A PRO* 3.9 31.6 - - + +
68A VAL* 4.5 6.5 - - + -
69A LEU* 3.7 20.0 - - + -
113A GLY 2.9 20.1 + - - +
114A TYR* 3.7 4.9 - - - +
116A ALA* 1.3 75.9 - - - +
118A ARG* 1.3 64.0 + - - +
121A ARG* 3.2 24.4 + - - +
145A MET* 4.1 22.7 - - + +
146A LEU* 3.9 15.7 - - + -
149A ALA* 4.2 13.9 - - + -
151A LEU* 3.8 10.7 - - + +
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Residues in contact with ARG 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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66A GLN* 5.9 0.4 + - - -
69A LEU* 4.1 19.0 - - + +
73A ASP* 4.5 0.6 + - - -
85A VAL* 5.0 1.6 - - + -
87A ASP* 3.0 28.3 + - - +
90A GLY* 3.3 31.0 + - - +
91A GLN* 3.6 9.9 - - - +
93A MET* 5.3 8.5 - - + -
94A ASP* 2.9 39.4 + - - +
114A TYR* 3.0 51.9 + - - +
115A SER* 3.5 9.9 - - - +
117A VAL* 1.3 78.4 - - - +
119A MET* 1.3 64.6 + - + +
121A ARG* 2.8 39.5 + - - +
122A LEU* 3.9 5.5 - - - +
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Residues in contact with MET 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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93A MET* 3.8 23.8 - - + -
97A ILE* 4.2 29.8 - - + +
105A VAL* 4.2 15.5 - - + -
107A GLU* 3.9 35.4 - - + +
115A SER* 2.9 23.2 + - - +
116A ALA 4.3 1.1 - - - +
118A ARG* 1.3 77.3 - - + +
120A ALA* 1.3 65.1 + - - +
122A LEU* 3.0 15.7 + - - +
123A LEU* 3.4 17.5 + - + +
129A LEU* 4.3 13.5 - - + -
180A MET* 5.6 2.7 - - - +
182A PHE* 4.0 28.3 - - + -
210A LEU* 6.3 0.9 - - - -
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Residues in contact with ALA 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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116A ALA 2.9 20.4 + - - +
119A MET* 1.3 78.7 - - - +
121A ARG* 1.3 62.5 + - - +
122A LEU 3.1 1.2 + - - -
123A LEU* 3.3 25.9 + - + +
129A LEU* 4.5 2.9 - - + +
146A LEU* 4.6 0.2 - - + -
151A LEU* 4.1 19.1 - - + -
154A LYS* 3.8 19.6 - - + +
155A VAL* 3.6 28.9 - - + -
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Residues in contact with ARG 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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65A PRO* 4.0 29.2 - - + -
66A GLN* 4.1 18.6 + - - +
69A LEU* 3.8 21.6 - - - +
94A ASP* 2.9 40.2 + - - -
98A ARG* 4.9 4.6 - - - +
117A VAL 3.2 17.5 + - - +
118A ARG* 2.8 45.0 + - - +
119A MET 3.2 0.8 - - - -
120A ALA* 1.3 76.8 - - - +
122A LEU* 1.3 77.3 + - + +
123A LEU 3.5 2.9 - - - +
151A LEU* 4.0 11.8 - - + +
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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