Contacts of the helix formed by residues 109 - 124 (chain B) in PDB entry 4H7Y
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 ASN 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B ARG* 3.4 13.9 - - - +
104B GLU* 2.8 41.9 + - - +
105B LEU* 4.1 1.0 + - - -
107B GLN* 3.6 19.8 + - - +
108B GLY* 1.3 78.6 - - - +
110B VAL* 1.3 59.7 + - - +
111B LYS 3.4 1.8 - - - -
112B LYS* 3.4 13.2 + - + +
113B SER* 3.0 26.3 + - - -
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 3.7 20.6 - - + -
108B GLY* 3.2 13.8 + - - +
109B ASN* 1.3 69.1 - - - +
111B LYS* 1.3 70.7 + - + +
113B SER* 3.2 8.5 + - - -
114B LYS* 3.0 22.2 + - + +
138B LEU* 4.2 20.4 - - + +
141B GLN* 6.6 0.4 - - + -
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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
----------------------------------------------------------
109B ASN 3.4 0.6 - - - -
110B VAL* 1.3 78.8 - - + +
112B LYS* 1.3 58.8 + - - +
114B LYS* 3.2 9.2 + - - +
115B GLN* 2.9 27.9 + - - +
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ARG* 6.5 0.2 - - - +
87B ARG* 5.6 4.0 - - - +
100B PHE* 5.3 4.9 - - - -
104B GLU* 3.7 29.4 - - + +
109B ASN* 3.4 20.5 + - + +
110B VAL 3.3 0.2 - - - -
111B LYS* 1.3 75.0 - - - +
113B SER* 1.3 66.1 + - - +
115B GLN* 2.8 32.1 + - - +
116B LEU* 2.9 48.5 + - + +
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA* 2.8 39.6 + - - +
104B GLU* 4.2 2.4 - - - +
105B LEU* 3.8 15.5 - - - +
109B ASN 3.0 14.7 + - - -
110B VAL* 3.4 11.0 - - - -
112B LYS* 1.3 76.2 - - - +
114B LYS* 1.3 62.0 + - - +
116B LEU* 3.4 2.6 + - - +
117B LEU* 3.1 27.5 + - - +
138B LEU* 4.2 12.5 - - - +
145B LEU* 3.9 6.9 - - - +
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 3.0 10.9 + - + +
111B LYS* 3.2 9.8 + - - +
113B SER* 1.3 76.2 - - - +
115B GLN* 1.3 60.1 + - - +
117B LEU* 3.4 4.1 + - - +
118B GLN* 3.0 64.0 + - - +
135B LEU* 4.3 10.5 - - + -
138B LEU* 3.5 24.4 - - + +
139B ASN* 5.3 10.2 + - - -
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Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 4.7 4.2 - - - +
111B LYS 2.9 16.5 + - - +
112B LYS* 2.8 38.7 + - - +
114B LYS* 1.3 76.0 - - - +
116B LEU* 1.3 73.2 + - - +
118B GLN* 3.3 7.8 + - - +
119B LYS* 2.8 40.2 + - + +
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Residues in contact with LEU 116 (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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87B ARG* 3.3 35.1 + - - +
97B HIS* 4.6 11.5 + - + +
100B PHE* 3.6 40.2 - - + -
101B ALA* 3.8 17.9 - - + +
104B GLU* 3.7 20.6 - - + -
112B LYS* 2.9 36.9 + - - +
113B SER 3.6 4.3 - - - +
115B GLN* 1.3 81.2 - - - +
117B LEU* 1.3 63.6 + - - +
119B LYS* 3.4 3.0 + - - +
120B ALA* 3.0 24.3 + - - +
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Residues in contact with LEU 117 (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 HIS 4.6 1.3 - - - +
98B ILE* 3.8 29.8 - - + +
101B ALA* 3.7 18.6 - - + -
113B SER 3.1 14.4 + - - +
114B LYS 3.7 5.6 - - - +
115B GLN 3.3 0.2 - - - -
116B LEU* 1.3 77.5 - - - +
118B GLN* 1.3 58.1 + - - +
120B ALA* 3.2 7.0 + - - +
121B VAL* 3.1 31.3 + - - +
131B LEU* 4.2 9.2 - - + +
134B ALA* 3.9 35.2 - - + +
135B LEU* 3.8 18.2 - - + +
138B LEU* 4.1 18.8 - - + -
145B LEU* 4.2 11.2 - - + -
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Residues in contact with GLN 118 (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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114B LYS* 3.0 55.1 + - - +
115B GLN* 3.9 6.8 - - - +
117B LEU* 1.3 73.0 - - - +
119B LYS* 1.3 65.8 + - - +
121B VAL* 3.3 9.2 + - - +
122B GLU* 3.0 31.1 + - + +
135B LEU* 3.9 18.3 - - + +
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Residues in contact with LYS 119 (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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87B ARG* 5.1 8.7 - - - +
97B HIS* 5.7 1.3 - - + +
115B GLN* 2.8 31.9 + - + +
116B LEU* 3.7 4.9 - - - +
118B GLN* 1.3 76.2 - - - +
120B ALA* 1.3 57.3 + - - +
122B GLU* 3.2 6.8 + - - +
123B ARG* 2.9 43.8 + - + +
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Residues in contact with ALA 120 (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 HIS* 3.5 41.4 + - + -
116B LEU 3.0 13.4 + - - +
117B LEU 3.3 10.5 - - - +
118B GLN 3.2 0.2 - - - -
119B LYS* 1.3 77.2 - - - +
121B VAL* 1.3 61.4 + - - +
123B ARG* 3.4 2.6 + - - -
124B GLY 3.1 4.0 + - - -
125B ALA* 3.0 28.6 + - + -
131B LEU* 3.6 18.6 - - + -
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Residues in contact with VAL 121 (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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117B LEU 3.1 17.8 + - - +
118B GLN* 3.6 8.7 - - - +
119B LYS 3.3 0.2 - - - -
120B ALA* 1.3 75.7 - - - +
122B GLU* 1.3 76.4 + - - +
124B GLY* 3.2 12.3 + - - -
125B ALA 5.1 0.4 - - - +
128B LEU* 4.1 22.4 - - + +
131B LEU* 3.9 28.5 - - + -
132B GLU* 5.7 1.8 - - + -
135B LEU* 4.1 17.9 - - + -
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Residues in contact with GLU 122 (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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118B GLN* 3.0 21.5 + - + +
119B LYS* 3.2 8.0 + - - +
121B VAL* 1.3 89.7 - - - +
123B ARG* 1.3 67.6 + - + +
124B GLY 3.2 0.6 + - - -
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Residues in contact with ARG 123 (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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91B LYS* 6.1 7.6 - - + +
97B HIS* 5.7 7.0 - - + +
119B LYS* 2.9 27.8 + - + +
120B ALA* 4.2 4.5 - - - +
121B VAL 3.3 0.4 - - - -
122B GLU* 1.3 81.7 - - + +
124B GLY* 1.3 61.1 + - - +
125B ALA* 3.5 2.4 + - + +
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Residues in contact with GLY 124 (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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92B LYS* 4.6 1.7 - - - +
120B ALA 3.1 3.2 + - - -
121B VAL 3.2 12.2 + - - -
122B GLU 3.2 1.8 + - - -
123B ARG* 1.3 79.4 - - - +
125B ALA* 1.3 67.5 + - - +
126B VAL* 3.6 14.2 + - - +
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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