Contacts of the helix formed by residues 101 - 113 (chain S) in PDB entry 4UJ3
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 101 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19S ASP* 2.7 40.8 + - - +
97S LEU* 3.0 40.5 + - - +
98S THR 4.3 1.8 - - - +
99S TYR 3.2 0.4 - - - -
100S GLU* 1.3 73.6 - - - +
102S VAL* 1.3 65.3 + - - +
103S GLU 3.1 2.7 - - - -
104S ARG* 2.9 24.3 + - + +
105S TRP* 3.0 18.6 + - - +
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Residues in contact with VAL 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89S LEU* 3.6 27.3 - - + +
91S TYR* 4.0 15.0 - - + -
98S THR 3.5 13.4 + - - +
99S TYR* 2.9 33.7 + - + +
101S ASN* 1.3 77.1 - - - +
103S GLU* 1.3 56.9 + - - +
105S TRP* 3.2 2.3 + - - -
106S LEU* 2.9 27.0 + - + +
121S LEU* 3.7 31.2 - - + -
142S PHE* 4.0 23.1 - - + -
148S LEU* 5.7 0.4 - - + -
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Residues in contact with GLU 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100S GLU 3.6 11.5 + - - +
101S ASN 3.1 0.2 - - - -
102S VAL* 1.3 81.0 - - - +
104S ARG* 1.3 62.1 + - - +
106S LEU* 3.2 9.3 + - - +
107S LYS* 3.0 23.3 + - - +
142S PHE* 4.7 17.1 - - + -
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Residues in contact with ARG 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100S GLU 4.6 0.2 + - - -
101S ASN* 2.9 23.9 + - + +
103S GLU* 1.3 79.2 - - - +
105S TRP* 1.3 61.1 + - + +
107S LYS* 3.4 8.3 + - - +
108S GLU* 3.1 26.0 + - - +
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Residues in contact with TRP 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S ILE* 4.1 12.0 - - + +
18S GLY* 3.5 37.9 - - - -
19S ASP* 2.5 33.3 + - - +
69S GLY* 3.0 30.1 - - - -
71S GLU* 3.7 41.5 - - + -
81S TYR* 4.4 13.5 - - - -
89S LEU* 3.7 23.1 - - + -
98S THR 5.5 1.3 - - - -
101S ASN* 3.0 27.0 + - - +
102S VAL* 3.6 6.7 - - - +
104S ARG* 1.3 77.4 - - + +
106S LEU* 1.3 59.1 + - - +
107S LYS 3.1 0.2 - - - -
108S GLU* 3.3 9.2 + - + +
109S LEU* 2.9 30.0 + - - +
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Residues in contact with LEU 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89S LEU* 3.7 15.1 - - + +
102S VAL 2.9 16.1 + - - +
103S GLU* 3.5 7.4 - - - +
105S TRP* 1.3 76.4 - - - +
107S LYS* 1.3 60.5 + - - +
109S LEU* 3.5 5.7 + - + +
110S ARG* 3.2 59.4 + - + +
119S ILE* 4.0 26.9 - - + -
142S PHE* 4.2 17.7 - - + -
146S ASN* 4.1 12.1 - - + +
148S LEU* 4.0 31.4 - - + -
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Residues in contact with LYS 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103S GLU 3.0 12.2 + - - +
104S ARG* 3.4 13.2 - - - +
106S LEU* 1.3 74.8 - - - +
108S GLU* 1.3 65.9 + - - +
109S LEU 3.2 0.5 + - - -
110S ARG* 3.4 8.5 + - - +
111S ASP* 3.2 33.2 + - - +
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Residues in contact with GLU 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S GLU* 5.4 2.7 - - - +
81S TYR* 4.3 17.3 - - + +
104S ARG 3.1 10.4 + - - +
105S TRP* 3.3 17.5 + - + +
107S LYS* 1.3 78.3 - - - +
109S LEU* 1.3 63.6 + - - +
111S ASP* 4.6 1.3 - - - -
112S HIS* 3.1 42.7 + - + +
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Residues in contact with LEU 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S VAL* 5.1 0.2 - - + -
17S ILE* 3.7 25.4 - - + -
81S TYR* 3.1 36.5 + - + -
87S ALA* 3.9 17.3 - - + -
89S LEU* 4.9 0.9 - - + -
105S TRP 2.9 14.2 + - - +
106S LEU* 3.5 11.4 - - + +
107S LYS 3.1 0.2 - - - -
108S GLU* 1.3 73.3 - - - +
110S ARG* 1.3 57.7 + - - +
111S ASP 3.0 4.3 - - - -
113S ALA* 2.8 43.8 + - + +
117S ILE* 5.1 3.4 - - + -
119S ILE* 3.2 48.0 - - + -
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Residues in contact with ARG 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M GLU* 4.7 23.3 - - - +
142M PHE* 5.3 10.3 - - + -
145M LYS* 4.1 13.2 + - - +
146M ASN* 5.5 2.1 + - - -
106S LEU* 3.2 48.8 + - + +
107S LYS* 3.4 6.2 + - - +
109S LEU* 1.3 80.6 - - + +
111S ASP* 1.3 64.7 + - - +
113S ALA 4.4 5.3 - - - +
114S ASP 6.1 0.2 - - - -
117S ILE* 6.5 0.4 - - + -
119S ILE* 4.8 9.9 - - + -
146S ASN* 3.6 31.3 + - - -
148S LEU* 5.8 0.2 - - - +
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Residues in contact with ASP 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142M PHE* 5.9 2.8 - - - -
145M LYS* 3.0 26.2 - - - +
107S LYS* 3.2 21.6 - - - +
108S GLU* 4.6 0.7 - - - -
109S LEU 3.0 0.4 - - - -
110S ARG* 1.3 87.0 - - - +
112S HIS* 1.3 80.4 + - + +
113S ALA 3.5 0.4 - - - -
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Residues in contact with HIS 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145M LYS* 4.7 2.5 - - - -
77S THR* 3.2 24.9 + - - -
78S SER* 4.3 22.5 + - - +
81S TYR* 3.6 30.8 - + + +
82S ARG* 5.1 0.7 + - - -
108S GLU* 3.1 26.4 + - + +
111S ASP* 1.3 92.7 - - + +
113S ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145M LYS* 2.6 27.0 + - - -
81S TYR* 4.1 28.0 - - + +
109S LEU* 2.8 29.2 + - + +
110S ARG* 4.4 4.5 - - - +
112S HIS* 1.3 80.2 - - - +
114S ASP* 1.3 67.0 + - - +
115S SER 3.6 0.2 + - - -
117S ILE* 4.3 15.0 - - + -
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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