Contacts of the helix formed by residues 111 - 124 (chain B) in PDB entry 3H5O
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 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B SER* 3.0 19.9 + - - +
109B HIS 3.7 5.6 - - - +
110B TYR* 1.3 78.0 - - - +
112B ALA* 1.3 66.1 + - - +
113B GLY* 3.1 10.3 + - - -
114B GLN* 2.8 59.3 + - - +
115B GLU* 2.9 12.9 + - - +
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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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110B TYR 4.1 1.8 + - - -
111B ASP* 1.3 70.7 - - - +
113B GLY* 1.3 62.6 + - - +
115B GLU* 3.6 12.9 - - - +
116B LEU* 3.0 25.5 + - - +
136B SER 5.5 0.7 - - - +
137B HIS* 4.4 7.9 - - - -
138B ALA* 3.9 29.4 + - + +
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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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111B ASP* 3.0 10.7 + - - -
112B ALA* 1.3 79.8 - - - +
114B GLN* 1.3 61.4 + - - +
116B LEU* 3.6 5.2 + - - +
117B GLN* 3.3 20.4 + - - +
138B ALA* 5.8 1.6 - - - -
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Residues in contact with GLN 114 (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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97A ASP* 4.5 9.8 + - - +
107B ASN 4.5 1.4 - - - +
108B SER* 3.8 15.3 + - - +
109B HIS* 3.3 29.0 + - - +
111B ASP* 2.8 35.1 + - - +
113B GLY* 1.3 71.5 - - - +
115B GLU* 1.3 60.3 + - - +
116B LEU 3.2 0.4 - - - -
117B GLN* 3.6 10.3 - - - +
118B LEU* 2.8 40.3 + - + +
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Residues in contact with GLU 115 (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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76B LEU* 4.0 25.0 - - + +
108B SER* 3.7 25.7 - - - -
111B ASP 2.9 8.1 + - - +
112B ALA* 3.2 13.6 + - - +
114B GLN* 1.3 76.2 - - - +
116B LEU* 1.3 58.4 + - - +
118B LEU* 3.3 6.5 + - - +
119B LEU* 2.9 28.1 + - - +
132B ILE* 3.7 11.1 - - - +
133B THR 4.3 5.0 + - - +
136B SER 4.3 1.2 - - - +
137B HIS* 2.7 49.9 + - - +
138B ALA 5.0 0.2 + - - -
141B PHE* 4.0 11.8 - - + -
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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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112B ALA 3.0 15.3 + - - +
113B GLY* 3.8 6.3 - - - +
115B GLU* 1.3 77.4 - - - +
117B GLN* 1.3 62.1 + - - +
119B LEU* 3.1 5.1 + - + +
120B ARG* 3.1 59.9 + - + +
138B ALA* 3.8 20.0 - - + -
140B PRO* 3.6 25.6 - - + -
141B PHE* 4.3 21.2 - - + -
144B ILE* 3.7 17.3 - - + -
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Residues in contact with GLN 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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102A GLN* 4.3 11.6 + - - +
113B GLY 3.3 11.8 + - - +
114B GLN* 3.3 15.5 + - - +
116B LEU* 1.3 79.6 - - - +
118B LEU* 1.3 61.4 + - + +
120B ARG* 4.1 9.0 - - - +
121B ALA* 3.1 24.3 + - - +
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Residues in contact with LEU 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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102A GLN* 3.7 26.2 - - - +
103A MSE 5.9 1.6 - - - +
76B LEU* 4.0 15.5 - - + -
106B GLY* 4.1 11.0 - - - -
107B ASN 3.4 40.8 - - - +
108B SER* 3.8 9.0 - - - +
114B GLN* 2.8 26.7 + - + +
115B GLU* 3.5 4.7 - - - +
116B LEU 3.2 0.2 - - - -
117B GLN* 1.3 75.9 - - + +
119B LEU* 1.3 67.9 + - - +
121B ALA* 3.2 3.3 + - - +
122B TYR* 3.1 40.7 + - + +
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Residues in contact with LEU 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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74B LEU* 4.3 21.3 - - + -
76B LEU* 4.7 4.4 - - + +
115B GLU 2.9 13.7 + - - +
116B LEU* 3.1 12.8 + - + +
118B LEU* 1.3 77.8 - - - +
120B ARG* 1.3 64.4 + - + +
122B TYR* 3.2 2.1 + - - +
123B LEU* 2.9 41.2 + - + +
127B PRO* 6.5 0.2 - - + -
130B VAL* 4.9 9.4 - - + -
141B PHE* 3.4 26.5 - - + +
144B ILE* 4.2 14.6 - - + -
145B LEU* 3.2 35.4 - - + -
150B LEU* 4.9 5.8 - - + -
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Residues in contact with ARG 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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116B LEU* 3.1 47.2 + - + +
117B GLN* 4.1 6.8 - - - +
119B LEU* 1.3 79.6 - - + +
121B ALA* 1.3 64.5 + - - +
123B LEU* 3.0 29.8 + - + +
124B GLN* 3.6 4.9 + - - +
140B PRO* 4.4 9.1 - - - +
144B ILE* 3.6 29.0 - - + +
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Residues in contact with ALA 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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102A GLN* 3.6 35.4 - - + +
117B GLN 3.1 20.6 + - - +
118B LEU 3.4 5.4 - - - +
119B LEU 3.2 0.4 - - - -
120B ARG* 1.3 77.9 - - - +
122B TYR* 1.3 61.5 + - + +
124B GLN* 3.8 14.2 + - - +
125B HIS* 4.5 6.9 + - - -
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Residues in contact with TYR 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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102A GLN* 3.9 16.8 + - - -
103A MSE 3.5 10.4 + - - -
104A LEU* 3.2 35.0 - - + +
122A TYR* 5.6 1.7 + + - -
125A HIS* 4.4 12.8 - + - -
74B LEU* 4.0 35.4 - - + -
104B LEU* 4.2 36.1 - - + -
105B ILE 3.2 22.2 + - - -
106B GLY* 4.8 0.8 - - - -
118B LEU* 3.1 41.7 + - + +
119B LEU 4.0 0.2 - - - +
121B ALA* 1.3 75.0 - - + +
123B LEU* 1.3 65.0 - - - +
124B GLN 3.1 2.2 - - - -
125B HIS* 3.0 20.5 + - - +
126B ARG 3.4 5.7 + - - -
127B PRO* 3.7 10.1 - - + +
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Residues in contact with LEU 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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119B LEU* 2.9 20.3 + - + +
120B ARG* 3.0 28.4 + - + +
122B TYR* 1.3 78.1 - - - +
124B GLN* 1.3 53.3 + - - +
126B ARG* 2.7 31.6 + - + +
127B PRO* 4.6 7.6 - - + -
144B ILE* 3.5 20.9 - - + -
148B HIS* 3.4 45.3 - - + +
150B LEU* 3.4 33.0 - - + -
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Residues in contact with GLN 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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126A ARG* 4.4 16.4 + - - -
120B ARG 3.6 5.2 + - - +
121B ALA 4.0 9.6 - - - +
122B TYR 3.1 0.4 - - - -
123B LEU* 1.3 79.5 - - - +
125B HIS* 1.3 86.7 + - + +
126B ARG* 3.2 9.2 + - - +
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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