Contacts of the helix formed by residues 104 - 119 (chain A) in PDB entry 3C2B
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 GLY 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASP 3.3 8.0 + - - -
101A VAL* 3.2 13.6 + - - -
103A ALA* 1.3 75.0 - - - +
105A ASP* 1.3 60.8 + - - -
106A VAL 3.3 2.2 - - - -
107A SER* 3.4 6.0 + - - -
108A LEU* 2.8 32.4 + - - +
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.8 29.5 - - + +
103A ALA 3.6 3.1 + - - -
104A GLY* 1.3 70.8 - - - -
106A VAL* 1.3 86.3 + - - +
108A LEU* 3.4 9.0 + - - +
109A ALA* 2.9 29.5 + - - +
112A ARG* 4.8 2.1 + - - +
120B ARG* 4.7 14.0 - - + -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.1 20.6 - - + -
27A VAL* 3.9 17.0 - - + -
68A GLN* 3.4 39.5 - - - +
71A LYS* 5.5 3.1 - - - +
104A GLY 3.3 0.4 - - - -
105A ASP* 1.3 92.1 + - - +
107A SER* 1.3 61.8 + - - +
109A ALA* 3.2 1.3 + - + +
110A LEU* 2.8 44.6 + - + +
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 5.0 4.3 - - - +
101A VAL* 3.7 30.0 + - - +
102A LEU* 4.2 9.1 + - - +
104A GLY* 3.4 7.1 + - - -
106A VAL* 1.3 79.8 - - - +
108A LEU* 1.3 63.2 + - - +
110A LEU* 3.3 5.4 + - - -
111A ASN* 2.9 42.5 + - - +
175A HIS* 5.0 1.9 + - - -
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU 3.3 17.7 - - - +
103A ALA* 3.6 18.4 - - - +
104A GLY 2.8 23.1 + - - +
105A ASP* 3.7 8.1 - - - +
107A SER* 1.3 77.7 + - - +
109A ALA* 1.3 51.4 + - - +
111A ASN* 3.4 0.4 + - - +
112A ARG* 2.8 63.5 + - - +
175A HIS* 4.0 6.5 - - + -
178A MSE 3.8 30.3 - - + +
179A LEU* 3.6 29.2 - - + +
120B ARG* 6.5 0.2 - - - -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.1 32.0 - - + +
27A VAL* 3.9 28.3 - - + +
105A ASP 2.9 18.2 + - - +
106A VAL* 3.2 4.2 + - + +
108A LEU* 1.3 75.1 - - - +
110A LEU* 1.3 57.9 + - - +
112A ARG* 3.4 16.8 + - - +
113A LEU* 2.9 24.3 + - - +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.5 4.5 - - + -
26A LEU* 3.9 17.5 - - + -
64A MSE 4.4 25.6 - - + +
65A ILE* 4.2 29.4 - - + +
68A GLN* 3.7 26.2 - - + -
106A VAL* 2.8 45.3 + - + +
107A SER* 4.0 5.2 - - - +
109A ALA* 1.3 74.6 - - - +
111A ASN* 1.3 56.5 + - - +
113A LEU* 3.1 10.2 + - + +
114A ALA* 2.9 31.1 + - - +
129A LEU* 4.6 12.8 - - + +
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Residues in contact with ASN 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 6.1 0.2 - - - +
107A SER* 2.9 40.5 + - - +
108A LEU 3.7 3.1 - - - +
110A LEU* 1.3 71.5 - - - +
112A ARG* 1.3 58.9 + - - +
114A ALA* 3.3 5.1 + - - +
115A ILE* 2.8 39.1 + - + +
129A LEU* 4.1 20.4 - - - +
175A HIS* 4.4 19.2 + - - -
179A LEU* 3.8 18.8 - - + -
176B VAL* 4.7 1.9 - - - +
180B LEU* 3.9 23.2 - - - +
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Residues in contact with ARG 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 5.8 0.4 - - - +
30A GLY* 6.4 0.2 - - - -
105A ASP* 4.8 1.8 + - - +
108A LEU* 2.8 50.0 + - - +
109A ALA* 3.5 17.1 - - - +
111A ASN* 1.3 72.4 - - - +
113A LEU* 1.3 63.7 + - - +
115A ILE* 3.4 0.9 + - - +
116A GLY 3.1 18.2 + - - -
178A MSE 2.8 27.5 + - - -
179A LEU* 2.9 26.2 + - + +
181A GLY* 4.2 5.5 - - - -
115B ILE* 3.5 25.6 - - + +
116B GLY* 3.6 13.8 - - - +
118B ALA* 3.5 27.4 - - - +
119B SER* 3.3 12.9 + - - +
120B ARG* 3.3 30.5 + - - +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.1 27.1 - - + -
31A GLU* 3.6 38.6 - - + +
34A LEU* 5.8 3.6 - - + -
57A ARG* 5.2 2.0 - - - +
61A LEU* 3.9 42.2 - - + +
64A MSE 5.0 4.5 - - + -
65A ILE* 5.2 3.4 - - + -
109A ALA 2.9 15.9 + - - +
110A LEU* 3.1 19.3 + - + +
112A ARG* 1.3 79.3 - - - +
114A ALA* 1.3 62.0 + - - +
116A GLY* 3.3 2.4 + - - -
117A GLN* 3.2 29.2 + - + +
125A LEU* 4.3 9.4 - - + -
116B GLY 5.4 0.2 - - - -
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 4.7 1.6 - - + -
110A LEU 2.9 15.7 + - - +
111A ASN 3.9 0.4 - - - +
113A LEU* 1.3 73.9 - - - +
115A ILE* 1.3 63.0 + - - +
117A GLN* 3.4 3.8 + - - +
118A ALA* 3.2 23.6 + - - +
125A LEU* 4.2 24.0 - - + +
126A GLY 4.7 4.2 + - - -
129A LEU* 3.5 26.9 - - + -
180B LEU* 3.6 18.1 - - + +
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ASN* 2.8 26.8 + - + +
112A ARG 3.9 2.9 - - - +
114A ALA* 1.3 70.2 - - - +
116A GLY* 1.3 64.4 + - - +
117A GLN 3.2 1.0 + - - -
118A ALA* 3.3 14.6 + - - +
119A SER* 4.2 0.7 + - - -
179A LEU* 3.7 29.6 - - + -
112B ARG* 3.6 40.0 - - + +
115B ILE* 3.7 24.7 - - + -
176B VAL* 4.6 6.1 - - + -
179B LEU* 3.9 32.1 - - + +
180B LEU* 3.7 24.2 - - + -
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Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU* 6.3 3.1 - - - -
112A ARG 3.1 11.3 + - - -
113A LEU 3.3 4.4 + - - -
115A ILE* 1.3 76.8 - - - +
117A GLN* 1.3 63.7 + - - +
119A SER* 3.8 11.3 + - - +
112B ARG 4.2 6.5 - - - -
116B GLY* 3.7 22.2 - - - -
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU* 4.6 12.1 - - - +
57A ARG* 3.8 19.0 + - - +
58A ASP* 4.1 13.5 + - - -
61A LEU* 3.9 17.8 - - + +
113A LEU* 3.2 19.3 + - + +
114A ALA 3.8 6.7 - - - +
115A ILE 3.1 1.2 - - - -
116A GLY* 1.3 79.2 - - - +
118A ALA* 1.3 65.8 + - - +
119A SER 3.2 4.7 + - - +
120A ARG 3.3 20.4 - - - +
125A LEU* 3.7 33.7 - - + +
126A GLY 6.1 0.2 - - - +
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ALA 3.2 15.9 + - - +
115A ILE 3.3 4.4 + - - +
117A GLN* 1.3 76.9 - - - +
119A SER* 1.3 51.1 + - - +
120A ARG* 2.8 20.3 + - - +
126A GLY* 5.5 2.9 - - - +
112B ARG* 4.2 6.6 + - - +
179B LEU 3.5 25.4 - - - +
180B LEU 3.6 21.1 - - - +
181B GLY* 4.2 6.0 - - - +
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ILE 4.2 0.9 + - - -
116A GLY 3.8 15.1 + - - +
117A GLN 3.8 2.6 - - - +
118A ALA* 1.3 70.6 - - - +
120A ARG* 1.3 71.0 + - - +
109B ALA* 6.3 1.3 - - - -
112B ARG* 3.7 41.0 - - - +
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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