Contacts of the helix formed by residues 101 - 116 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284B ARG* 5.4 1.4 - - - +
99C GLU* 4.6 21.5 + - + +
100C THR* 1.3 80.1 + - - +
102C ILE* 1.3 62.6 + - - +
103C ILE 3.2 1.8 - - - -
104C PRO* 3.0 20.0 - - - +
105C ARG* 3.5 27.4 + - - +
159C ASP* 3.2 14.6 + - - +
119D GLU* 3.4 21.6 + - - +
122D ARG* 3.0 49.4 - - - +
123D LEU* 3.8 25.1 - - + -
126D ALA* 5.5 0.7 - - - -
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Residues in contact with ILE 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C THR* 2.6 24.3 + - - +
101C ARG* 1.3 73.1 - - - +
103C ILE* 1.3 72.1 + - + +
105C ARG* 3.0 21.6 - - - +
106C VAL* 3.0 9.6 + - - +
140C PHE* 4.0 20.9 - - + -
144C VAL* 3.6 31.0 - - + -
113D TRP* 3.4 53.8 - - + -
123D LEU* 4.7 6.9 - - + +
128D VAL* 4.6 10.3 - - + -
133D LEU* 4.6 10.8 - - + -
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C PHE* 6.0 2.9 - - + -
100C THR* 3.3 30.3 + - + +
102C ILE* 1.3 81.8 - - + +
104C PRO* 1.4 71.4 - - + +
105C ARG 2.7 5.8 + - - -
106C VAL* 2.9 25.7 + - + +
107C LEU* 3.0 22.2 + - + +
140C PHE* 5.3 0.4 - - + -
141C ILE* 4.0 34.3 - - + -
144C VAL* 4.2 9.9 - - + -
145C ILE* 4.1 21.5 - - + -
157C ASN* 4.0 15.3 - - - +
159C ASP* 5.1 0.4 - - - +
162C THR* 4.5 9.9 - - + -
169C LEU* 6.0 1.3 - - + -
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Residues in contact with PRO 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG* 3.0 26.5 - - - +
103C ILE* 1.4 94.2 - - + +
105C ARG* 1.3 53.6 + - - +
107C LEU* 3.4 15.6 - - + +
108C ALA* 2.9 30.1 + - - +
159C ASP* 3.9 25.8 - - + +
161C PHE* 4.7 20.2 - - + +
162C THR* 4.7 8.1 - - + +
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Residues in contact with ARG 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B THR 3.1 26.7 + - - -
195B ARG* 4.2 15.0 + - - +
101C ARG* 3.7 27.7 + - - +
102C ILE* 3.0 15.1 - - - +
103C ILE 2.7 0.6 + - - -
104C PRO* 1.3 80.3 - - - +
106C VAL* 1.3 64.0 + - - +
107C LEU 3.1 1.2 + - - -
108C ALA* 3.2 16.9 + - - +
109C MET* 3.2 20.9 + - + +
113D TRP* 2.9 48.3 - - + +
119D GLU* 3.7 27.1 + - - -
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ILE 3.0 10.1 + - - +
103C ILE* 2.9 21.9 + - + +
105C ARG* 1.3 79.6 - - - +
107C LEU* 1.3 56.9 + - + +
109C MET* 3.2 27.6 - - + +
110C ARG* 2.9 28.9 + - - +
137C MET* 3.7 18.8 - - + +
140C PHE* 3.4 46.2 - - + -
141C ILE* 4.7 5.4 - - + -
106D VAL* 6.2 0.4 - - + -
109D MET* 4.3 2.0 - - + -
113D TRP* 4.3 14.4 - - + -
140D PHE* 6.5 0.4 - - + -
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ILE* 3.0 31.9 + - + +
104C PRO* 3.4 17.3 - - + +
106C VAL* 1.3 73.9 - - - +
108C ALA* 1.3 68.2 + - - +
109C MET 3.0 1.6 - - - -
110C ARG* 3.0 5.0 + - + +
111C GLN* 2.8 26.3 + - - +
137C MET* 4.4 10.1 - - + -
141C ILE* 4.9 3.8 - - + -
161C PHE 5.5 0.2 - - - +
162C THR* 4.3 21.8 - - + -
165C SER* 4.3 21.5 - - - +
168C TYR* 4.2 22.0 - - + -
169C LEU* 4.1 25.8 - - + -
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PRO 2.9 13.5 + - - +
105C ARG* 3.5 10.5 - - - +
107C LEU* 1.3 74.1 - - - +
109C MET* 1.3 58.7 + - + +
111C GLN* 3.1 9.7 - - - +
112C ALA* 3.0 25.3 + - - +
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Residues in contact with MET 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ARG* 3.3 25.6 - - + +
106C VAL* 3.2 29.8 - - + +
107C LEU 3.0 0.2 - - - -
108C ALA* 1.3 74.8 - - + +
110C ARG* 1.3 65.1 - - - +
112C ALA* 2.7 20.6 + - - +
113C TRP* 3.0 47.2 + - + +
137C MET* 6.0 0.7 - - + -
106D VAL* 4.6 3.4 - - + -
109D MET* 3.2 47.3 - - + +
140D PHE* 6.4 0.7 - - + -
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Residues in contact with ARG 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL 2.9 16.4 + - - +
107C LEU* 3.4 5.8 - - + +
109C MET* 1.3 79.8 - - - +
111C GLN* 1.3 72.2 + - - +
113C TRP* 3.0 27.3 + - + +
114C SER* 2.9 34.7 + - - +
130C ASP* 3.9 13.5 + - - +
133C LEU* 3.3 35.9 - - + +
134C ASP* 2.8 23.4 + - - -
137C MET* 3.7 26.9 - - + -
168C TYR* 2.6 42.7 + - + +
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Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU 2.8 15.1 + - - +
108C ALA* 3.1 14.6 - - - +
110C ARG* 1.3 76.1 - - - +
112C ALA* 1.3 56.2 + - - +
114C SER* 2.7 11.5 + - - -
115C LYS* 2.6 73.1 + - + +
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Residues in contact with ALA 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ALA 3.0 9.4 + - - +
109C MET* 2.7 21.0 + - - +
111C GLN* 1.3 78.3 - - - +
113C TRP* 1.3 67.3 + - + +
115C LYS* 3.2 20.9 + - - +
116C SER* 3.4 8.5 + - - -
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Residues in contact with TRP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL 5.0 0.2 - - - -
109C MET* 3.0 52.5 + - + +
110C ARG* 3.4 30.1 - - + +
112C ALA* 1.3 82.1 - - + +
114C SER* 1.3 58.4 + - - +
116C SER* 3.3 20.3 + - - -
119C GLU* 4.3 11.5 - - + +
120C LYS* 4.1 12.6 + - - -
123C LEU* 4.5 18.0 - - + +
133C LEU* 4.2 16.4 - - + -
137C MET* 5.1 5.8 - - - -
102D ILE* 3.2 30.5 - - + -
105D ARG* 3.1 50.0 - - + +
106D VAL* 4.3 9.6 - - + -
109D MET* 4.9 1.1 - - - -
140D PHE* 5.3 4.3 - + - -
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Residues in contact with SER 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ARG* 2.9 31.8 + - - -
111C GLN* 2.7 18.9 + - - -
113C TRP* 1.3 71.8 - - - +
115C LYS* 1.3 51.1 + - - -
116C SER 2.7 28.5 + - - +
120C LYS* 4.9 9.8 - - - +
130C ASP* 3.8 13.9 + - - -
133C LEU* 4.5 3.1 - - - +
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Residues in contact with LYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLN* 2.6 55.1 + - + +
112C ALA* 3.4 17.0 - - - +
114C SER* 1.3 70.9 - - - +
116C SER* 1.3 57.3 + - - +
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Residues in contact with SER 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ALA 3.4 7.9 + - - -
113C TRP 3.3 17.3 - - - -
114C SER 2.7 18.3 - - - +
115C LYS* 1.3 79.9 - - - +
117C GLY* 1.3 60.6 + - - +
118C ARG* 2.8 2.6 + - - +
119C GLU* 2.7 37.2 + - - -
120C LYS* 2.9 18.6 + - - +
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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