Contacts of the helix formed by residues 99 - 111 (chain B) in PDB entry 2FHP
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 ASP 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B LYS* 6.1 2.5 - - - +
98B MSE 1.3 76.9 - - - +
100B ALA* 1.3 60.4 + - - +
101B ASN* 2.9 32.6 + - - +
102B ARG* 3.0 46.1 + - - +
103B ALA* 2.9 26.9 + - - +
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Residues in contact with ALA 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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48B LEU* 3.7 35.1 - - + +
49B TYR* 3.8 29.8 - - + +
70B ILE* 4.2 5.6 - - + +
98B MSE 3.5 2.6 + - - -
99B ASP* 1.3 74.4 + - - +
101B ASN* 1.3 63.7 + - - +
103B ALA* 3.2 16.5 + - - +
104B LEU* 3.3 13.0 + - - +
131B GLN* 4.2 3.8 - - - +
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Residues in contact with ASN 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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99B ASP* 2.9 14.0 + - - +
100B ALA* 1.3 73.9 - - - +
102B ARG* 1.3 64.6 + - - +
104B LEU* 3.3 19.4 + - - +
105B GLU* 3.4 17.3 + - - +
127B GLU* 2.9 31.3 + - - -
131B GLN* 3.0 33.0 + - - +
134B LYS* 4.3 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 MSE 3.6 18.0 - - + +
99B ASP* 3.0 42.4 + - + +
101B ASN* 1.3 73.6 - - - +
103B ALA* 1.3 65.5 + - - +
105B GLU* 3.1 23.4 + - - +
106B GLN* 3.0 18.5 + - - +
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Residues in contact with ALA 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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48B LEU* 4.2 1.6 - - + -
70B ILE* 3.8 35.9 - - + -
98B MSE 3.6 16.5 - - + +
99B ASP 2.9 12.9 + - - +
100B ALA 3.3 12.1 - - - +
101B ASN 3.2 0.4 - - - -
102B ARG* 1.3 77.6 - - - +
104B LEU* 1.3 57.5 + - - +
106B GLN* 3.2 3.0 + - - +
107B PHE* 2.9 42.1 + - + -
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Residues in contact with LEU 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 LEU* 4.1 11.7 - - + -
48B LEU* 4.5 11.4 - - + -
100B ALA 3.3 11.0 + - - +
101B ASN* 3.3 13.6 + - - +
102B ARG 3.2 0.8 - - - -
103B ALA* 1.3 76.4 - - - +
105B GLU* 1.3 61.8 + - + +
107B PHE* 3.5 19.2 + - + +
108B TYR* 3.4 16.8 + - - +
131B GLN* 4.2 31.2 - - + +
134B LYS* 4.9 13.0 - - + -
135B MSE 4.0 38.8 - - + -
138B ARG* 5.6 2.5 - - + +
140B LEU* 3.7 17.9 - - + +
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Residues in contact with GLU 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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101B ASN 3.6 14.1 - - - +
102B ARG* 3.1 23.6 + - - +
104B LEU* 1.3 75.7 - - + +
106B GLN* 1.3 63.8 + - - +
108B TYR* 3.2 17.1 + - - +
109B GLU* 3.4 16.4 + - - +
138B ARG* 6.3 1.8 - - - +
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Residues in contact with GLN 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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96B ARG* 3.2 24.6 + - - +
98B MSE 3.3 27.6 - - + +
102B ARG 3.0 13.2 + - - +
103B ALA 3.7 6.7 - - - +
105B GLU* 1.3 75.9 - - - +
107B PHE* 1.3 64.3 + - - +
109B GLU* 3.1 12.9 + - + +
110B GLU* 3.1 35.7 + - + +
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Residues in contact with PHE 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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46B LEU* 3.5 41.3 - - + -
48B LEU* 4.8 0.2 - - + -
68B ILE* 3.9 16.6 - - + -
70B ILE* 3.8 19.5 - - + -
96B ARG* 3.6 19.3 - - - -
103B ALA* 2.9 31.1 + - + -
104B LEU* 3.7 20.9 - - + +
105B GLU 3.3 0.2 - - - -
106B GLN* 1.3 76.7 - - - +
108B TYR* 1.3 63.5 + - - +
110B GLU* 3.3 15.4 + - - -
111B LYS 3.0 18.0 + - - -
112B LEU* 3.2 24.5 + - + -
114B PHE* 3.6 20.0 - + + -
140B LEU* 4.1 15.2 - - + +
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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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111A LYS* 3.6 47.5 + - + +
113A GLN* 5.9 3.1 - - - +
104B LEU 3.4 8.0 + - - +
105B GLU* 3.2 11.6 + - - +
106B GLN 3.1 0.8 - - - -
107B PHE* 1.3 79.8 - - - +
109B GLU* 1.3 79.1 + - - +
111B LYS* 3.1 20.3 + - - +
138B ARG* 3.1 79.1 + - + +
139B GLN* 3.8 13.2 + - - -
140B LEU* 4.0 7.8 - - + +
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Residues in contact with GLU 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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105B GLU 3.8 12.2 - - - +
106B GLN* 3.1 14.1 + - + +
108B TYR* 1.3 96.2 - - - +
110B GLU* 1.3 62.0 + - + +
111B LYS* 3.3 15.3 + - - +
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Residues in contact with GLU 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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96B ARG* 2.6 46.5 + - - -
106B GLN* 3.1 29.4 + - + +
107B PHE* 3.7 13.8 - - - +
108B TYR 3.2 0.2 - - - -
109B GLU* 1.3 75.6 - - + +
111B LYS* 1.3 68.7 + - - +
112B LEU* 3.4 23.0 + - + +
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Residues in contact with LYS 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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110A GLU* 3.0 29.5 + - - +
111A LYS* 3.1 38.3 + - + +
112A LEU* 4.3 9.8 - - - +
107B PHE 3.0 4.4 + - - -
108B TYR* 3.1 14.9 + - - +
109B GLU* 3.9 10.0 + - - +
110B GLU* 1.3 80.9 - - - +
112B LEU* 1.3 65.3 + - - +
113B GLN* 3.9 4.7 + - - +
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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