Contacts of the helix formed by residues 97 - 113 (chain B) 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 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B MET* 4.7 13.4 - - - +
98B LEU* 1.3 74.6 + - + +
99B GLU* 3.0 17.6 + - + +
100B GLU* 3.1 37.3 + - - +
101B THR* 2.9 28.7 + - - -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B MET* 4.2 19.5 - - + -
97B THR* 1.3 78.7 - - + +
99B GLU* 1.3 65.0 + - - +
101B THR* 4.0 8.0 - - + -
102B ARG* 3.3 34.0 + - + +
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B THR* 3.0 14.5 - - + +
98B LEU* 1.3 85.1 - - + +
100B GLU* 1.3 65.3 + - + +
102B ARG* 3.3 6.6 + - - +
103B GLU* 3.0 45.5 + - - +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B THR* 3.1 43.8 + - - +
99B GLU* 1.3 73.5 - - - +
101B THR* 1.3 54.7 + - - +
103B GLU* 3.5 12.5 + - - +
104B ASN* 2.7 52.5 + - - +
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PRO* 4.7 15.3 - - + +
76B ILE* 5.1 0.7 - - + -
78B ASP* 3.6 32.9 - - + +
81B GLY 5.7 0.9 - - - -
82B MET* 3.5 21.3 - - - +
97B THR 2.9 21.6 + - - -
98B LEU* 4.0 9.6 - - + -
99B GLU 3.2 0.2 - - - -
100B GLU* 1.3 78.3 - - - +
102B ARG* 1.3 61.0 + - + +
104B ASN* 3.3 5.7 + - - +
105B ALA* 2.8 28.9 + - - +
127B TYR* 4.8 10.5 - - + -
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 3.3 30.1 - - + +
99B GLU* 3.3 11.6 + - - +
100B GLU 3.3 0.4 - - - -
101B THR* 1.3 83.0 - - + +
103B GLU* 1.3 61.1 + - + +
105B ALA* 3.4 7.7 + - - +
106B LYS* 3.1 51.4 + - - +
127B TYR* 4.5 26.5 + - - -
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 3.0 46.5 + - - +
100B GLU* 3.2 11.3 + - - +
102B ARG* 1.3 76.3 - - + +
104B ASN* 1.3 62.9 + - - +
106B LYS* 3.2 14.1 + - + +
107B THR* 3.0 28.5 + - - -
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Residues in contact with ASN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PRO* 2.9 32.4 + - + +
47B THR* 4.4 4.6 - - - +
49B PRO* 3.6 28.3 - - + +
100B GLU* 2.7 34.7 + - - +
101B THR* 3.7 3.7 - - - +
103B GLU* 1.3 73.0 - - - +
105B ALA* 1.3 61.5 + - - +
107B THR* 3.0 5.8 + - - -
108B TYR* 2.8 32.3 + - - +
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PRO* 5.6 1.3 - - - +
76B ILE* 4.4 18.2 - - + -
101B THR 2.8 17.0 + - - +
102B ARG 3.5 6.1 - - - +
103B GLU 3.3 0.2 - - - -
104B ASN* 1.3 76.5 - - - +
106B LYS* 1.3 59.1 + - + +
108B TYR* 3.8 5.0 - - - +
109B VAL* 2.9 38.1 + - + +
125B LEU* 6.1 0.2 - - - -
127B TYR* 3.3 38.1 - - + +
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Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ARG* 3.1 42.8 + - - +
103B GLU* 3.3 13.0 - - + +
104B ASN 3.1 0.2 - - - -
105B ALA* 1.3 78.4 - - + +
107B THR* 1.3 57.0 + - - +
109B VAL* 4.0 3.8 - - - +
110B ALA* 2.8 33.3 + - - +
127B TYR* 5.9 0.9 - - - +
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Residues in contact with THR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PRO* 3.7 24.5 - - + +
50B ASP* 4.6 5.8 - - - +
103B GLU 3.0 15.6 + - - -
104B ASN* 3.0 10.0 + - - -
106B LYS* 1.3 76.3 - - - +
108B TYR* 1.3 62.3 + - - +
110B ALA* 3.4 5.5 + - - +
111B GLN* 3.1 45.1 + - - +
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 3.7 24.9 - - - +
44B ALA* 3.6 23.6 - - + +
45B ASP 5.2 3.8 - - - -
46B PRO* 6.5 1.3 - - + -
48B ARG 4.0 14.6 - - - -
49B PRO* 3.5 14.3 + - + +
51B LEU* 3.5 32.2 - - + +
55B HIS* 5.3 6.3 - + - +
59B LEU* 4.0 9.7 - - - +
74B LEU* 3.4 34.0 - - + +
76B ILE* 4.5 9.9 - - + -
104B ASN 2.8 20.1 + - - +
105B ALA* 3.8 5.4 - - - +
107B THR* 1.3 73.8 - - - +
109B VAL* 1.3 60.4 + - - +
111B GLN* 3.3 3.6 + - - +
112B ALA* 2.8 37.7 + - + +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 4.5 7.9 - - + -
76B ILE* 4.8 1.8 - - + -
105B ALA 2.9 27.3 + - - +
106B LYS* 4.0 4.7 - - - +
108B TYR* 1.3 74.4 - - + +
110B ALA* 1.3 68.8 + - - +
112B ALA* 3.8 4.7 - - + +
113B GLY* 3.0 21.1 + - - -
118B GLN* 3.7 20.9 + - - +
123B PHE* 5.0 7.2 - - + -
125B LEU* 3.7 42.0 - - + -
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LYS 2.8 20.9 + - - +
107B THR* 3.7 6.1 - - - +
109B VAL* 1.3 79.3 - - - +
111B GLN* 1.3 66.1 + - + +
113B GLY* 3.4 10.1 + - - -
114B LYS* 4.0 7.3 + - - +
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PRO 4.3 2.0 - - - -
50B ASP* 3.8 9.1 + - - +
51B LEU* 2.8 54.3 + - + +
107B THR* 3.1 36.9 + - - +
108B TYR 3.9 0.2 - - - +
110B ALA* 1.3 78.3 - - + +
112B ALA* 1.3 64.6 + - - +
114B LYS* 3.1 29.3 + - + +
115B ILE 4.3 0.7 + - - -
243B LEU* 4.4 6.7 - - + +
244B THR* 3.6 37.4 + - + +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 3.5 11.2 - - + +
59B LEU* 4.6 9.0 - - + -
74B LEU* 4.7 2.9 - - + -
108B TYR* 2.8 41.4 + - + +
109B VAL* 3.3 7.2 + - - +
111B GLN* 1.3 72.7 - - - +
113B GLY* 1.3 56.4 + - - +
114B LYS 3.0 0.4 - - - -
115B ILE* 3.0 8.6 + - - +
116B LEU* 2.9 45.5 + - + +
118B GLN* 5.2 1.3 - - - +
123B PHE* 6.1 0.9 - - + -
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL 3.0 15.7 + - - -
110B ALA 3.4 5.1 + - - -
111B GLN 3.1 1.0 - - - -
112B ALA* 1.3 72.3 - - - +
114B LYS* 1.3 61.8 + - - +
115B ILE 3.1 2.2 - - - -
116B LEU 3.8 10.3 - - - -
118B GLN* 4.0 18.6 - - - +
303B PRO 4.2 1.9 - - - +
304B GLN* 3.1 29.8 + - - +
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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