Contacts of the helix formed by residues 108 - 121 (chain A) in PDB entry 4L57
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 CYS 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A PHE* 3.8 28.0 - - + +
101A PRO* 3.8 7.2 - - - -
102A LEU* 3.6 24.5 - - + +
104A LYS 4.3 6.5 - - - +
105A TYR* 3.0 15.9 + - - +
107A HIS* 1.3 81.2 - - - +
109A VAL* 1.3 68.2 + - - +
110A GLY 3.5 0.7 - - - -
111A GLU* 3.4 1.8 + - - +
112A LYS* 3.0 55.4 + - - +
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PRO* 3.6 31.0 - - + -
105A TYR* 3.2 26.8 + - + +
106A HIS 4.7 0.6 + - - +
108A CYS* 1.3 77.4 - - - +
110A GLY* 1.3 64.5 + - - +
112A LYS* 3.3 9.7 + - - +
113A TYR* 3.3 25.2 + - + -
130A LEU* 3.7 25.8 - - + -
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Residues in contact with GLY 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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106A HIS 5.2 4.0 + - - -
107A HIS 5.3 0.2 - - - -
108A CYS 3.5 0.4 - - - +
109A VAL* 1.3 82.7 - - - +
111A GLU* 1.3 63.1 + - - +
113A TYR* 3.3 9.3 + - - +
114A ARG* 3.0 22.5 + - - +
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Residues in contact with GLU 111 (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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68A PRO* 3.7 7.1 - - - +
69A GLY* 2.7 32.1 + - - -
70A PHE 3.5 0.5 + - - -
71A PHE* 3.2 19.1 + - + -
72A LEU* 2.9 41.0 + - + +
107A HIS* 3.0 31.6 + - - +
108A CYS 3.4 1.4 + - - +
109A VAL 3.3 1.0 - - - -
110A GLY* 1.3 76.9 - - - +
112A LYS* 1.3 57.8 + - - +
114A ARG* 3.4 7.3 + - - +
115A TRP* 2.9 29.6 + - - +
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Residues in contact with LYS 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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11A MET* 3.6 28.5 - - + +
12A ASP* 2.9 33.3 + - - -
71A PHE* 3.9 17.1 - - + -
99A THR* 2.9 30.3 + - + +
100A SER 3.8 11.0 - - - -
108A CYS* 3.0 43.8 + - - +
109A VAL 3.7 4.7 - - - +
110A GLY 3.2 0.2 - - - -
111A GLU* 1.3 77.5 - - - +
113A TYR* 1.3 66.3 + - + +
115A TRP* 3.3 2.8 + - - +
116A VAL* 3.1 29.1 + - - +
128A ILE* 4.8 2.0 - - + -
130A LEU* 4.3 15.7 - - + -
202A PO4 3.5 1.6 + - - -
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Residues in contact with TYR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A VAL* 3.3 18.1 + - + +
110A GLY* 3.3 11.7 + - - +
112A LYS* 1.3 79.6 - - + +
114A ARG* 1.3 57.5 + - - +
116A VAL* 3.3 4.0 + - - +
117A GLU* 2.9 27.8 + - - +
125A VAL* 3.7 31.0 - - + +
128A ILE* 3.6 48.5 + - + +
130A LEU* 4.0 30.9 + - + +
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Residues in contact with ARG 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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72A LEU* 3.5 26.0 - - + -
110A GLY 3.0 16.1 + - - +
111A GLU* 3.8 2.2 - - - +
113A TYR* 1.3 73.8 - - - +
115A TRP* 1.3 59.3 + - - +
117A GLU* 3.0 34.2 + - - -
118A GLN* 2.9 62.5 + - - +
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Residues in contact with TRP 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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11A MET* 3.6 25.6 - - + -
15A LEU* 3.4 38.4 - - + -
16A ALA* 3.8 16.6 - - + -
71A PHE 3.4 15.3 - - - +
72A LEU* 3.4 29.8 - - - +
74A LEU* 2.8 23.4 + - + +
76A PRO* 4.0 16.8 - - + -
81A LEU* 4.0 18.8 - - + -
111A GLU 2.9 18.3 + - - +
112A LYS* 3.6 5.6 - - - +
114A ARG* 1.3 75.5 - - - +
116A VAL* 1.3 67.4 + - + +
118A GLN* 4.8 1.3 - - - -
119A HIS* 2.9 64.5 + + + -
120A LEU* 5.0 4.5 - - + -
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Residues in contact with VAL 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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11A MET* 3.8 21.5 - - + -
15A LEU* 5.9 0.2 - - + -
97A ILE* 4.0 19.7 - - + -
112A LYS 3.1 13.8 + - - +
113A TYR 3.7 6.5 - - - +
115A TRP* 1.3 82.8 - - + +
117A GLU* 1.3 66.0 + - - +
120A LEU* 2.8 26.6 + - + +
121A GLY 3.1 5.2 + - - -
124A PHE* 3.7 20.2 - - + +
125A VAL* 3.7 27.1 - - + +
128A ILE* 3.8 15.7 - - + -
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Residues in contact with GLU 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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113A TYR 2.9 14.6 + - - +
114A ARG* 3.0 39.4 + - - +
116A VAL* 1.3 76.9 - - - +
118A GLN* 1.3 59.8 + - - +
121A GLY* 2.9 25.5 + - - -
122A PRO* 4.5 18.6 - - + +
125A VAL* 3.5 20.1 - - + +
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Residues in contact with GLN 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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72A LEU* 3.9 24.6 - - - +
114A ARG* 2.9 56.8 + - - +
115A TRP* 3.9 2.9 - - - +
117A GLU* 1.3 78.8 - - - +
119A HIS* 1.3 71.4 + - + +
121A GLY 4.8 0.2 + - - -
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Residues in contact with HIS 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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72A LEU 4.7 3.8 + - - -
74A LEU 4.2 4.1 + - - -
76A PRO* 3.8 29.8 - - + +
81A LEU* 3.9 24.6 - - + +
115A TRP* 2.9 75.6 + + + +
118A GLN* 1.3 87.1 + - + +
120A LEU* 1.3 64.2 + - + +
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Residues in contact with LEU 120 (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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15A LEU* 4.5 6.7 - - + -
81A LEU* 3.9 31.9 - - + +
84A VAL* 3.6 34.1 - - + -
85A ARG* 4.2 15.4 - - + +
97A ILE* 4.0 25.6 - - + -
115A TRP* 5.0 6.1 - - + -
116A VAL* 2.8 19.0 + - + +
119A HIS* 1.3 78.2 - - + +
121A GLY* 1.3 51.3 + - - +
123A GLN* 2.5 31.2 + - - -
124A PHE* 3.4 25.8 - - + -
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Residues in contact with GLY 121 (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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116A VAL 3.1 2.1 + - - +
117A GLU* 2.9 23.2 + - - -
118A GLN 4.6 0.4 + - - -
119A HIS 3.9 0.2 - - - -
120A LEU* 1.3 76.6 - - - +
122A PRO* 1.3 77.7 - - - +
123A GLN* 3.2 7.6 - - - -
124A PHE* 3.1 12.6 + - - +
125A VAL* 3.3 12.1 + - - +
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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