Contacts of the helix formed by residues 101 - 116 (chain B) in PDB entry 3AP3
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 ARG 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ALA* 5.0 8.3 - - - -
99B GLU* 4.3 20.1 + - + +
100B THR* 1.3 82.9 + - - +
102B ILE* 1.3 59.7 + - - +
103B ILE 3.6 1.1 - - - -
104B PRO* 3.7 12.1 - - - +
105B ARG* 3.4 29.9 + - - +
159B ASP* 3.2 14.9 + - - +
196C LYS* 2.9 70.0 + - + +
198C THR* 4.3 18.8 + - - +
284C ARG* 5.8 0.4 - - - +
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Residues in contact with ILE 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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113A TRP* 3.5 47.6 - - + -
128A VAL* 4.3 17.3 - - + -
133A LEU* 4.3 13.0 - - + -
100B THR* 3.1 21.5 + - - +
101B ARG* 1.3 79.1 - - - +
103B ILE* 1.3 72.9 - - + +
105B ARG* 2.8 31.6 - - - +
106B VAL* 2.9 17.9 + - + +
140B PHE* 4.5 8.3 - - + -
144B VAL* 4.3 15.7 - - + -
196C LYS* 4.5 8.7 - - - +
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Residues in contact with ILE 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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72B PHE* 5.8 4.3 - - + -
100B THR* 3.5 20.6 + - + +
102B ILE* 1.3 78.4 - - + +
104B PRO* 1.3 73.6 - - + +
106B VAL* 2.9 26.9 - - - +
107B LEU* 3.1 23.9 + - + +
140B PHE* 5.4 1.1 - - + -
141B ILE* 4.1 31.4 - - + -
144B VAL* 3.8 22.4 - - + -
145B ILE* 3.9 17.5 - - + -
157B ASN* 3.6 25.1 - - - +
159B ASP* 4.9 0.2 - - - +
162B THR* 4.7 9.0 - - + -
169B LEU* 6.0 1.3 - - + -
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Residues in contact with PRO 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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101B ARG* 3.7 17.0 - - - +
102B ILE 3.6 0.7 - - - -
103B ILE* 1.3 97.4 - - + +
105B ARG* 1.3 61.2 + - - +
107B LEU* 3.3 17.3 + - + +
108B ALA* 3.0 24.8 + - - +
159B ASP* 4.0 29.2 - - + +
161B PHE* 5.0 9.9 - - + +
162B THR* 4.5 16.8 - - + +
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Residues in contact with ARG 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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113A TRP* 3.2 43.9 - - + +
101B ARG* 3.4 23.0 + - - +
102B ILE* 2.8 20.6 + - + +
104B PRO* 1.3 82.9 - - - +
106B VAL* 1.3 59.5 + - - +
108B ALA* 3.3 12.6 + - - +
109B MET* 3.3 19.5 + - + +
193C ILE* 3.1 39.3 + - - +
196C LYS* 3.3 38.4 - - - +
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Residues in contact with VAL 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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109A MET* 4.5 1.1 - - + -
113A TRP* 4.3 6.7 - - + -
140A PHE* 6.4 1.6 - - + -
102B ILE* 2.9 26.9 + - + +
103B ILE* 2.9 28.7 - - - +
105B ARG* 1.3 73.0 - - - +
107B LEU* 1.3 53.9 + - + +
109B MET* 3.2 30.3 + - + +
110B ARG* 2.8 34.0 + - - +
137B MET* 4.2 18.2 - - + +
140B PHE* 3.7 41.1 - - + -
141B ILE* 5.0 2.7 - - + -
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Residues in contact with LEU 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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103B ILE* 3.1 34.2 + - + +
104B PRO* 3.3 19.1 - - + +
105B ARG 3.3 0.2 - - - -
106B VAL* 1.3 74.7 - - - +
108B ALA* 1.3 55.4 + - - +
110B ARG* 3.0 4.0 + - - +
111B GLN* 2.6 36.9 + - - +
137B MET* 3.7 25.4 - - + -
141B ILE* 4.2 6.1 - - + -
162B THR* 4.8 16.2 - - + +
165B SER* 5.0 17.0 - - - +
168B TYR* 4.3 15.7 - - + -
169B LEU* 3.9 28.3 - - + -
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Residues in contact with ALA 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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104B PRO 3.0 12.3 + - - +
105B ARG* 3.5 11.7 - - - +
106B VAL 3.3 0.2 - - - -
107B LEU* 1.3 75.5 - - - +
109B MET* 1.3 57.6 + - + +
111B GLN* 3.0 11.1 - - - +
112B ALA* 2.9 27.3 + - - +
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Residues in contact with MET 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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106A VAL* 4.7 2.5 - - + -
109A MET* 3.1 49.6 - - + +
113A TRP* 4.7 0.2 - - - -
140A PHE* 6.4 0.9 - - + -
105B ARG* 3.3 15.7 - - + +
106B VAL* 3.2 39.0 + - + +
107B LEU 3.1 0.4 - - - -
108B ALA* 1.3 73.9 - - + +
110B ARG* 1.3 64.5 + - - +
112B ALA* 2.9 10.8 + - - +
113B TRP* 2.9 54.8 + - + +
137B MET* 6.3 0.2 - - - -
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Residues in contact with ARG 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 VAL 2.8 13.8 + - - +
107B LEU* 3.4 7.4 - - - +
109B MET* 1.3 76.2 - - - +
111B GLN* 1.3 67.5 + - - +
113B TRP* 3.2 23.4 + - + +
114B SER* 2.8 41.9 + - - +
130B ASP* 3.4 17.0 + - - +
133B LEU* 3.2 37.0 - - + +
134B ASP* 2.9 21.0 + - - -
137B MET* 3.7 28.3 - - + -
168B TYR* 2.8 39.1 + - - -
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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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107B LEU 2.6 16.5 + - - +
108B ALA* 3.0 15.0 - - - +
110B ARG* 1.3 74.2 - - - +
112B ALA* 1.3 54.6 + - - +
114B SER* 3.0 9.2 + - - -
115B LYS* 2.5 75.0 + - + +
165B SER* 5.8 0.2 + - - -
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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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108B ALA 2.9 14.0 + - - +
109B MET* 2.9 13.4 + - - +
111B GLN* 1.3 74.9 - - - +
113B TRP* 1.3 58.0 + - + +
115B LYS* 2.9 9.6 + - - -
116B SER* 2.7 35.9 + - - -
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Residues in contact with TRP 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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102A ILE* 3.2 37.7 - - + -
105A ARG* 3.1 37.7 - - + +
106A VAL* 3.7 15.3 - - + -
109A MET* 4.7 1.8 - - - -
140A PHE* 4.7 8.5 - + - -
109B MET* 2.9 52.5 + - + +
110B ARG* 3.4 31.4 - - + +
111B GLN 3.2 0.2 - - - -
112B ALA* 1.3 80.2 - - + +
114B SER* 1.3 62.2 + - - +
116B SER* 3.1 21.4 - - - -
119B GLU* 4.5 10.1 - - + +
120B LYS* 4.1 12.6 + - - +
123B LEU* 4.1 17.5 - - + -
133B LEU* 4.1 17.7 - - + -
137B MET* 5.6 0.9 - - - -
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Residues in contact with SER 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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110B ARG* 2.8 31.1 + - - +
111B GLN* 3.0 12.2 + - - -
113B TRP* 1.3 73.9 - - - +
115B LYS* 1.3 57.2 + - - +
116B SER 2.9 21.9 - - - +
120B LYS* 4.4 23.3 - - - +
130B ASP* 3.7 13.5 + - - -
133B LEU* 4.6 2.6 - - - +
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Residues in contact with LYS 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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111B GLN* 2.5 63.9 + - + +
112B ALA* 2.9 10.1 + - - +
114B SER* 1.3 70.2 - - - +
116B SER* 1.3 60.6 + - - +
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Residues in contact with SER 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 2.7 9.6 + - - -
113B TRP* 3.1 17.9 - - - +
114B SER 2.9 15.0 - - - +
115B LYS* 1.3 81.6 - - - +
117B GLY* 1.3 69.3 + - - +
118B ARG* 3.1 2.3 + - - +
119B GLU* 2.8 34.5 + - - +
120B LYS* 4.2 8.5 - - - +
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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