Contacts of the helix formed by residues 113 - 125 (chain A) in PDB entry 1HOV
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A TRP* 4.7 0.2 - - - -
106A THR 3.1 26.3 + - - +
107A ASN* 5.3 3.4 + - - -
108A THR 5.7 1.3 - - - -
111A ASN 3.5 2.4 - - - +
112A TYR* 1.3 91.7 - - - +
114A LEU* 1.3 65.4 + - - +
115A PHE* 3.3 14.0 + - - +
116A LEU* 2.8 26.0 + - - +
117A VAL* 2.7 9.9 - - - +
144A TYR* 4.0 21.3 - - - -
145A THR* 5.4 0.8 + - - -
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Residues in contact with LEU 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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24A THR* 4.3 8.3 - - + -
27A LEU* 3.9 12.1 - - + -
32A VAL* 3.4 27.6 - - + -
35A ALA* 3.4 17.2 - - + +
36A PHE* 3.7 34.3 - - + -
99A PHE* 4.5 11.2 - - + -
105A TRP* 3.5 28.7 - - + +
106A THR 3.9 9.9 + - - +
107A ASN* 4.7 0.4 - - - +
113A SER* 1.3 71.1 - - - +
115A PHE* 1.3 59.3 + - - +
117A VAL* 3.2 9.6 - - + +
118A ALA* 2.9 25.7 + - + +
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Residues in contact with PHE 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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35A ALA* 3.5 27.7 - - + +
38A ARG* 4.6 12.1 - - + -
39A ALA* 3.6 19.3 - - - -
42A VAL* 3.3 46.9 - - + -
107A ASN* 5.2 8.7 - - + +
113A SER* 3.0 9.8 - - - +
114A LEU* 1.3 81.3 - - - +
116A LEU* 1.3 60.8 + - + +
118A ALA* 4.1 1.0 - - - +
119A ALA* 3.0 24.0 + - + +
145A THR* 4.6 13.9 - - - -
148A PHE* 4.3 23.3 - + + -
800A I52 4.5 8.1 - - + -
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Residues in contact with LEU 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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112A TYR 3.2 13.2 - - - +
113A SER* 2.8 19.9 + - - +
115A PHE* 1.3 74.2 - - + +
117A VAL* 1.3 67.4 + - - +
118A ALA 3.0 1.6 + - - -
119A ALA* 3.0 16.5 + - + +
120A HIS* 3.2 10.3 + - + +
142A TYR* 3.0 42.8 - - + +
143A THR 4.4 2.5 - - - +
144A TYR* 4.8 1.3 - - + -
145A THR* 3.4 45.5 - - + +
800A I52 3.9 35.0 - - + +
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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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83A LEU* 4.7 9.9 - - + +
84A ALA* 5.3 1.1 - - + +
99A PHE* 3.8 20.4 - - + -
105A TRP* 3.6 20.4 - - + -
112A TYR* 3.6 32.1 - - + +
113A SER 2.7 21.2 + - - +
114A LEU* 3.2 23.8 - - + +
116A LEU* 1.3 78.5 - - - +
118A ALA* 1.3 60.4 + - - +
120A HIS* 3.7 4.6 + - - +
121A GLU* 3.3 24.8 + - - +
142A TYR* 4.4 9.9 - - + +
800A I52 5.5 3.4 - - + -
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Residues in contact with ALA 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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36A PHE* 3.4 34.1 - - + -
39A ALA* 4.5 4.3 - - + -
99A PHE* 3.9 10.3 - - + -
114A LEU* 2.9 24.7 + - + +
115A PHE* 4.1 2.5 - - - +
117A VAL* 1.3 76.7 - - - +
119A ALA* 1.3 55.0 + - - +
121A GLU* 2.8 4.4 + - - -
122A PHE* 2.4 46.7 + - + -
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Residues in contact with ALA 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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39A ALA* 4.6 1.5 - - - +
42A VAL* 4.4 18.6 - - + -
43A TRP* 3.5 14.2 + - - +
115A PHE* 3.0 25.0 + - + +
116A LEU* 3.0 16.2 + - + +
118A ALA* 1.3 73.4 - - - +
120A HIS* 1.3 57.6 + - - +
122A PHE* 2.6 36.6 + - - +
123A GLY 3.0 4.2 + - - -
137A LEU* 5.0 6.1 - - + -
800A I52 4.9 7.9 - - + -
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Residues in contact with HIS 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 LEU* 3.2 8.1 + - + +
117A VAL* 3.8 8.5 - - - +
119A ALA* 1.3 77.3 - - - +
121A GLU* 1.3 66.3 + - + +
123A GLY* 2.8 19.2 + - - -
124A HIS* 3.2 13.2 + + - -
130A HIS* 3.9 2.7 - - - -
137A LEU* 3.3 32.1 + - - +
138A MET* 4.1 6.4 - - - +
139A ALA 3.8 6.3 - - - -
166A ZN 2.2 30.9 - - - -
800A I52 2.8 79.6 + + + +
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Residues in contact with GLU 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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84A ALA* 3.3 27.3 - - + +
85A HIS* 3.4 28.6 - - - +
86A ALA* 4.2 2.1 - - - +
97A SER* 4.6 12.8 + - - -
99A PHE* 4.5 9.0 - - + -
117A VAL 3.3 13.9 + - - +
118A ALA* 2.8 12.9 + - - +
120A HIS* 1.3 78.3 - - + +
122A PHE* 1.3 64.3 + - + +
123A GLY 3.1 0.4 - - - -
124A HIS* 3.8 10.8 - - - +
125A ALA* 3.2 25.6 + - - +
800A I52 2.7 37.8 + - + -
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Residues in contact with PHE 122 (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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18A TYR* 5.8 10.3 - + - -
36A PHE* 3.4 46.7 - + + -
39A ALA* 4.2 13.2 - - + -
40A PHE* 3.8 26.2 - - + -
43A TRP* 3.9 24.4 - - + +
51A PHE* 4.5 20.0 - + - -
61A ILE* 6.5 1.1 - - + -
63A ILE* 5.7 7.0 - - + -
99A PHE* 6.2 0.2 - + - -
118A ALA* 2.4 37.5 + - + +
119A ALA* 2.6 22.3 + - - +
121A GLU* 1.3 72.9 - - + +
123A GLY* 1.3 57.5 + - - -
125A ALA* 4.4 6.8 - - - +
126A MET* 3.9 15.6 - - - +
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Residues in contact with GLY 123 (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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43A TRP* 3.2 22.5 - - - -
119A ALA 3.0 4.0 + - - -
120A HIS 2.8 5.2 + - - -
122A PHE* 1.3 80.1 - - - +
124A HIS* 1.3 65.3 + - - +
125A ALA 3.4 0.2 - - - -
126A MET* 3.1 19.4 + - - +
127A GLY 3.8 2.8 + - - -
128A LEU* 4.4 3.1 + - - +
138A MET* 2.9 28.2 - - - +
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Residues in contact with HIS 124 (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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86A ALA* 4.8 8.0 + - + +
87A PHE 5.3 2.4 - - - +
88A ALA* 6.2 0.5 - - - -
89A PRO* 6.0 0.5 - - - +
120A HIS* 3.2 16.0 + + - +
121A GLU* 3.7 16.8 + - - +
123A GLY* 1.3 71.4 - - - +
125A ALA* 1.3 54.7 + - - +
126A MET 2.5 27.3 + - - +
127A GLY* 3.5 3.1 + - - -
128A LEU 4.3 10.1 + - - +
129A GLU* 4.5 21.9 + - + +
130A HIS* 2.6 23.2 + + - -
138A MET* 3.2 17.5 - - + +
166A ZN 2.3 26.6 - - - -
800A I52 2.6 24.0 + - + -
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Residues in contact with ALA 125 (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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11A TRP* 5.2 4.7 - - - +
61A ILE* 4.3 23.5 - - + +
86A ALA* 4.3 16.9 - - + +
87A PHE 5.1 4.7 - - - +
89A PRO* 4.9 7.6 - - - +
95A GLY* 4.7 13.0 - - - +
97A SER* 5.3 4.7 - - - +
121A GLU 3.2 17.7 + - - +
122A PHE* 4.5 7.0 - - - +
123A GLY 3.4 0.2 - - - -
124A HIS* 1.3 78.2 - - - +
126A MET* 1.3 71.8 + - + +
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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