Contacts of the helix formed by residues 101 - 113 (chain A) in PDB entry 1H3F
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 THR 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PRO* 4.8 12.4 - - + +
78A ASP* 3.6 36.9 + - + +
102A ARG* 1.3 72.7 + - + +
103A GLU* 3.0 7.6 + - - +
104A ASN* 3.2 24.6 + - - +
105A ALA* 2.7 37.1 + - + +
127A TYR* 5.2 5.6 - - + -
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Residues in contact with ARG 102 (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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101A THR* 1.3 89.0 - - + +
103A GLU* 1.3 62.3 + - + +
105A ALA* 3.5 5.3 - - - +
106A LYS* 3.1 47.4 + - - +
127A TYR* 4.4 26.1 + - - -
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Residues in contact with GLU 103 (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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101A THR 3.0 5.9 - - - +
102A ARG* 1.3 76.7 - - + +
104A ASN* 1.3 72.9 + - - +
106A LYS* 2.9 20.3 + - - +
107A THR* 3.0 15.2 + - - -
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Residues in contact with ASN 104 (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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46A PRO* 3.1 34.7 + - + +
47A THR* 5.1 2.0 - - - +
49A PRO* 3.8 24.3 - - + +
101A THR* 3.2 23.1 + - - +
103A GLU* 1.3 78.7 - - - +
105A ALA* 1.3 53.9 + - - +
107A THR* 2.9 6.1 + - - -
108A TYR* 2.7 37.5 + - - +
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Residues in contact with ALA 105 (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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46A PRO* 5.2 2.8 - - - +
76A ILE* 4.3 19.1 - - + -
101A THR 2.7 22.6 + - - +
102A ARG* 3.5 7.4 - - - +
104A ASN* 1.3 72.8 - - - +
106A LYS* 1.3 52.5 + - - +
108A TYR* 3.8 4.7 - - - +
109A VAL* 2.8 42.1 + - + +
127A TYR* 3.8 35.7 - - + +
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Residues in contact with LYS 106 (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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102A ARG* 3.1 32.9 + - - +
103A GLU* 2.9 12.4 + - - +
105A ALA* 1.3 82.1 - - + +
107A THR* 1.3 56.1 + - - +
109A VAL* 4.0 4.9 - - - +
110A ALA* 2.8 31.5 + - - +
127A TYR* 5.9 2.0 - - - +
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Residues in contact with THR 107 (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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49A PRO* 3.8 22.4 - - + -
50A ASP* 4.2 8.3 - - - +
103A GLU 3.0 11.6 + - - -
104A ASN* 2.9 10.4 + - - -
106A LYS* 1.3 74.3 - - - +
108A TYR* 1.3 65.5 + - - +
110A ALA* 3.4 5.2 + - - +
111A GLN* 3.0 45.7 + - - +
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Residues in contact with TYR 108 (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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42A LEU* 3.9 20.6 - - - +
44A ALA* 3.4 29.9 - - + +
45A ASP 5.3 2.9 - - - -
46A PRO* 6.1 3.8 - - + -
48A ARG 3.8 12.3 - - - -
49A PRO* 3.5 19.9 + - + +
51A LEU* 3.3 33.2 - - + +
55A HIS* 5.5 4.4 - + - +
59A LEU* 4.3 8.0 - - - +
74A LEU* 3.7 29.1 - - + +
76A ILE* 4.2 13.7 - - + -
104A ASN 2.7 20.3 + - - +
105A ALA* 3.8 4.5 - - - +
107A THR* 1.3 72.6 - - - +
109A VAL* 1.3 62.1 + - - +
111A GLN* 3.3 3.0 + - - +
112A ALA* 2.8 33.7 + - + +
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Residues in contact with VAL 109 (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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74A LEU* 4.8 2.0 - - + -
76A ILE* 4.2 11.0 - - + -
105A ALA* 2.8 33.5 + - + +
106A LYS* 4.0 4.9 - - - +
108A TYR* 1.3 76.5 - - + +
110A ALA* 1.3 64.1 + - - +
112A ALA* 3.3 5.5 + - - +
113A GLY* 3.3 18.0 + - - -
118A GLN* 4.3 15.7 - - - +
123A PHE* 5.1 7.4 - - + -
125A LEU* 3.7 44.6 - - + -
127A TYR* 5.2 0.2 - - - +
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Residues in contact with ALA 110 (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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106A LYS 2.8 21.2 + - - +
107A THR* 3.6 7.0 - - - +
108A TYR 3.3 0.2 - - - -
109A VAL* 1.3 79.7 - - - +
111A GLN* 1.3 64.4 + - + +
113A GLY* 3.5 9.4 + - - -
114A LYS* 4.1 6.9 + - - +
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Residues in contact with GLN 111 (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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49A PRO 4.5 0.4 - - - -
50A ASP* 3.5 18.5 + - - +
51A LEU* 2.7 55.9 + - + +
107A THR* 3.0 38.4 + - - +
108A TYR 3.9 0.9 - - - +
110A ALA* 1.3 75.8 - - + +
112A ALA* 1.3 65.4 + - - +
113A GLY 3.1 2.7 - - - -
114A LYS* 3.1 27.2 + - + +
115A ILE* 4.3 1.0 + - - +
243A LEU* 4.6 5.9 - - + +
244A THR* 3.6 36.1 + - + +
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Residues in contact with ALA 112 (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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51A LEU* 3.6 10.7 - - + +
59A LEU* 4.9 6.7 - - + -
74A LEU* 4.3 11.0 - - + -
108A TYR* 2.8 36.3 + - + +
109A VAL* 3.3 8.7 + - - +
111A GLN* 1.3 76.9 - - - +
113A GLY* 1.3 56.9 + - - +
114A LYS 3.1 0.2 - - - -
115A ILE* 3.1 6.9 + - - +
116A LEU* 2.8 40.9 + - + +
118A GLN* 5.0 1.8 - - - +
123A PHE* 5.8 0.7 - - + -
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Residues in contact with GLY 113 (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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109A VAL 3.3 8.5 + - - -
110A ALA 3.5 5.8 + - - -
111A GLN 3.1 1.4 - - - -
112A ALA* 1.3 75.0 - - - +
114A LYS* 1.3 62.4 + - - +
115A ILE 3.0 2.2 + - - -
116A LEU 3.3 10.7 - - - +
118A GLN* 4.0 19.7 - - - +
303A PRO 4.2 2.4 - - - +
304A GLN* 3.1 26.9 + - - +
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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