Contacts of the helix formed by residues 98 - 109 (chain B) 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 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B TYR* 3.8 24.4 - - - -
93B PHE* 3.7 4.8 - - - -
97B LYS* 1.3 77.2 - - - +
99B ALA* 1.3 57.2 + - - +
100B GLU* 2.9 13.6 + - - -
101B VAL* 2.7 25.2 + - - +
102B ALA* 2.9 13.5 + - - +
130B PRO* 3.5 9.5 - - - +
131B LEU* 4.8 1.7 - - - +
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Residues in contact with ALA 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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96B TYR* 3.2 19.4 + - + +
98B GLY* 1.3 76.6 - - - +
100B GLU* 1.3 56.2 + - - +
102B ALA* 3.5 4.4 + - - +
103B HIS* 3.0 30.3 + - - +
130B PRO* 3.2 24.9 - - + +
134B GLU* 6.3 0.4 - - - -
327B TRP* 4.0 11.4 - - + -
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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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39B SER* 4.6 2.1 + - - -
41B LEU* 3.7 32.8 - - + +
92B TRP* 3.6 23.2 - - + +
93B PHE* 3.2 33.3 + - - +
96B TYR* 3.1 18.3 - - + +
98B GLY 2.9 20.0 + - - -
99B ALA* 1.3 75.8 - - - +
101B VAL* 1.3 71.7 + - - +
103B HIS* 4.4 0.9 - - - -
104B PHE* 3.1 30.6 + - + +
327B TRP* 3.7 22.5 - - + -
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Residues in contact with VAL 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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39B SER* 5.8 0.4 - - - +
41B LEU* 5.4 5.6 - - + -
86B GLN* 3.8 31.9 - - + +
87B TYR* 4.1 24.0 - - + -
93B PHE* 4.9 0.4 - - + -
98B GLY* 2.7 17.8 + - - +
100B GLU* 1.3 90.4 - - + +
102B ALA* 1.3 64.5 + - - +
104B PHE* 5.5 0.2 - - - -
105B MET* 3.0 56.6 + - + +
131B LEU* 3.9 14.8 - - + -
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Residues in contact with ALA 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 GLY 2.9 8.0 + - - +
99B ALA* 4.0 7.0 - - - +
101B VAL* 1.3 76.8 - - - +
103B HIS* 1.3 63.5 + - - +
105B MET* 4.3 2.0 - - - +
106B ASN* 3.0 33.5 + - - +
130B PRO 3.6 23.8 - - - +
131B LEU* 4.0 15.8 - - + +
134B GLU* 3.8 24.7 - - + +
135B ALA* 4.3 2.0 - - - +
137B PHE* 5.4 0.2 - - - -
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Residues in contact with HIS 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 ALA 3.0 19.3 + - - +
100B GLU 4.0 1.8 - - - +
102B ALA* 1.3 79.9 - - - +
104B PHE* 1.3 82.6 + + - +
106B ASN* 3.7 5.8 - - - +
107B ALA* 3.1 27.6 + - + +
323B ASP* 2.4 34.8 + - - -
327B TRP* 3.4 27.8 - + + -
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Residues in contact with PHE 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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41B LEU* 3.5 20.0 - - + -
61B VAL* 4.0 28.7 - - + -
92B TRP* 4.3 4.0 - + - -
100B GLU* 3.1 28.5 + - + +
101B VAL* 4.8 0.4 - - - +
103B HIS* 1.3 93.3 - + - +
105B MET* 1.3 62.4 + - + +
107B ALA* 3.4 7.1 + - + +
108B LEU* 3.0 35.8 + - + +
320B ILE* 4.2 11.2 - - + -
323B ASP* 3.6 29.8 - - + -
324B ILE* 3.5 42.2 - - + -
327B TRP* 4.1 19.3 - + - -
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Residues in contact with MET 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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82B ASP* 3.7 25.8 - - + -
86B GLN* 3.6 21.1 - - - +
101B VAL* 3.0 42.6 + - + +
104B PHE* 1.3 73.8 - - - +
106B ASN* 1.3 65.8 + - - +
108B LEU* 3.4 1.4 + - + -
109B ARG 3.0 16.5 + - - -
110B TYR* 3.2 51.8 + - + -
113B MET* 3.8 14.4 - - + +
131B LEU* 5.1 0.2 - - - -
137B PHE* 3.6 36.3 - - + -
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Residues in contact with ASN 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 ALA* 3.0 26.0 + - - +
103B HIS* 3.7 6.9 - - - +
105B MET* 1.3 78.0 - - - +
107B ALA* 1.3 57.4 + - - +
109B ARG* 2.9 26.7 + - - +
134B GLU* 2.8 25.7 + - - +
135B ALA* 3.6 0.4 - - - -
136B LYS* 2.7 59.6 + - + +
137B PHE* 3.4 13.4 - - - -
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Residues in contact with ALA 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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65B PHE* 3.7 16.5 - - - -
103B HIS* 3.1 21.7 + - + +
104B PHE* 3.7 12.6 - - + +
105B MET 3.3 0.2 - - - -
106B ASN* 1.3 77.1 - - - +
108B LEU* 1.3 63.5 + - + +
109B ARG* 3.3 9.6 + - - +
320B ILE* 4.0 22.7 - - + -
323B ASP* 5.7 1.3 - - - +
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Residues in contact with LEU 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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61B VAL* 3.9 29.8 - - + +
64B LEU* 3.5 33.4 - - + -
65B PHE* 3.8 38.8 - - + -
68B VAL* 4.7 2.5 - - + +
72B ARG* 3.1 24.2 + - - -
80B LEU* 3.7 8.6 - - + +
104B PHE* 3.0 22.9 + - - +
105B MET* 3.9 4.7 - - + +
106B ASN 3.3 0.2 - - - -
107B ALA* 1.3 76.7 - - + +
109B ARG* 1.3 66.4 + - - +
110B TYR* 3.9 18.6 - - + -
320B ILE* 4.3 10.1 - - + -
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Residues in contact with ARG 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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65B PHE* 6.1 2.0 - - - -
72B ARG* 2.9 56.3 + - - +
105B MET 3.0 1.9 + - - -
106B ASN* 2.9 23.4 + - - +
107B ALA* 3.7 8.1 + - - +
108B LEU* 1.3 80.1 - - - +
110B TYR* 1.3 69.0 + - - +
111B ASP* 3.5 4.9 + - - +
137B PHE* 6.0 0.2 - - - -
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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