Contacts of the helix formed by residues 109 - 122 (chain A) in PDB entry 5VLR
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 VAL 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ASP* 2.8 24.0 + - - +
108A ARG* 1.3 80.6 - - - +
110A LYS* 1.4 54.6 + - - +
111A LYS 3.4 0.7 - - - -
112A LEU* 3.4 3.2 + - - +
113A ILE* 2.8 58.1 + - + +
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Residues in contact with LYS 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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107A ASP* 3.4 24.2 + - + +
109A VAL* 1.4 73.5 - - - +
111A LYS* 1.4 58.8 + - - +
113A ILE* 4.5 5.6 - - - +
114A ASN* 2.8 63.3 + - - +
673A ARG* 4.8 5.2 - - - +
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Residues in contact with LYS 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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81A GLU* 4.5 31.7 - - + +
107A ASP 3.3 16.5 + - - +
108A ARG* 4.5 5.2 - - + -
110A LYS* 1.4 78.5 - - - +
112A LEU* 1.4 60.2 + - - +
114A ASN* 4.3 2.8 - - - +
115A SER* 3.1 27.0 + - - -
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Residues in contact with LEU 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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81A GLU* 5.6 6.3 - - - +
83A GLU* 4.9 19.3 - - + -
108A ARG* 3.7 18.3 - - - +
109A VAL* 3.4 9.6 + - - +
110A LYS 3.3 0.4 - - - -
111A LYS* 1.4 75.7 - - - +
113A ILE* 1.3 65.5 + - + +
115A SER* 3.5 6.0 + - - -
116A GLN* 3.0 44.2 + - + +
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Residues in contact with ILE 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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109A VAL* 2.8 44.2 + - + +
110A LYS* 4.2 4.3 - - - +
112A LEU* 1.3 72.0 - - + +
114A ASN* 1.4 64.1 + - - +
116A GLN* 3.1 17.0 + - - +
117A ILE* 3.0 35.1 + - + +
673A ARG* 3.7 25.1 - - - +
676A THR* 3.9 26.7 - - + -
679A MET* 4.2 12.1 - - - -
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Residues in contact with ASN 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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78A GLU* 4.7 4.5 - - - +
110A LYS* 2.8 46.4 + - - +
111A LYS* 4.3 3.6 - - - +
113A ILE* 1.4 68.3 - - - +
115A SER* 1.3 60.2 + - - +
117A ILE* 3.5 5.0 + - - +
118A SER* 3.3 25.3 + - - -
125A LEU* 3.7 17.9 - - + +
140A ARG* 5.2 2.6 - - - +
673A ARG* 2.9 42.0 + - - +
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Residues in contact with SER 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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74A ASN* 4.9 4.8 + - - +
78A GLU* 4.5 10.1 + - - -
79A GLN 4.2 5.0 + - - -
80A GLN* 3.4 44.3 - - - +
81A GLU 4.3 5.2 + - - -
111A LYS 3.1 18.5 + - - -
112A LEU* 3.5 6.3 + - - -
113A ILE 3.2 0.4 - - - -
114A ASN* 1.3 73.5 - - - +
116A GLN* 1.4 66.5 + - - +
118A SER* 3.1 14.6 + - - -
119A LEU* 3.2 12.7 + - - +
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Residues in contact with GLN 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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80A GLN* 5.3 2.4 + - - +
112A LEU* 3.0 40.2 + - + +
113A ILE* 3.1 14.4 + - - +
115A SER* 1.4 77.1 - - - +
117A ILE* 1.4 56.0 + - - +
119A LEU* 3.3 8.6 + - - +
120A LEU* 2.9 30.0 + - - +
679A MET* 3.5 20.8 - - + +
680A LYS* 5.1 8.9 - - - +
683A MET* 3.2 44.2 - - + +
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Residues in contact with ILE 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 ILE* 3.0 21.4 + - + +
114A ASN* 3.6 7.2 - - - +
115A SER 3.2 0.2 - - - -
116A GLN* 1.4 73.8 - - - +
118A SER* 1.4 55.4 + - - +
120A LEU* 3.1 4.0 + - - +
121A ILE* 2.8 49.2 + - + +
125A LEU* 3.7 27.4 - - + -
669A GLU* 4.0 18.8 - - + +
672A CYS* 3.7 11.7 - - + -
673A ARG* 3.7 47.3 - - + +
679A MET* 3.5 20.6 - - + +
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Residues in contact with SER 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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74A ASN* 5.3 2.2 - - - -
76A THR* 3.6 18.4 - - - +
78A GLU* 3.2 19.1 + - - -
114A ASN 3.3 7.1 + - - -
115A SER 3.1 10.4 + - - -
117A ILE* 1.4 75.0 - - - +
119A LEU* 1.3 61.8 + - - +
121A ILE* 4.3 0.2 - - - -
122A GLY 3.3 1.6 + - - -
123A LYS 3.2 37.6 + - - -
124A GLY* 3.8 7.9 - - - -
125A LEU* 3.1 26.7 + - - +
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Residues in contact with LEU 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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74A ASN* 5.7 6.0 - - - +
76A THR* 4.6 8.2 - - - +
80A GLN* 6.3 2.0 - - - +
115A SER 3.2 8.2 + - - +
116A GLN* 3.5 11.4 - - - +
117A ILE 3.2 0.6 - - - -
118A SER* 1.3 79.2 - - - +
120A LEU* 1.3 62.0 + - - +
122A GLY* 3.2 14.0 + - - -
652A ARG* 4.3 3.3 + - - -
683A MET* 6.3 1.8 - - + -
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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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116A GLN 2.9 16.5 + - - +
117A ILE* 3.5 4.7 - - - +
119A LEU* 1.3 75.0 - - - +
121A ILE* 1.3 50.8 + - + +
648A PHE* 3.6 27.9 - - + -
649A TRP* 6.2 0.4 - - + -
652A ARG* 2.7 29.8 + - - -
672A CYS* 3.8 25.4 - - - -
679A MET* 3.9 35.0 - - + +
682A LEU* 3.5 35.2 - - + +
683A MET* 3.6 14.5 - - + +
686A GLY* 5.8 2.0 - - - -
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Residues in contact with ILE 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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117A ILE* 2.8 33.0 + - + +
120A LEU* 1.3 72.3 - - + +
122A GLY* 1.3 61.0 + - - +
123A LYS* 3.2 37.0 - - + +
125A LEU* 4.4 9.2 - - + -
128A PHE* 4.2 17.3 - - + -
648A PHE* 4.9 2.5 - - + -
652A ARG* 3.5 13.0 + - - +
655A MET* 3.4 26.9 - - + +
665A GLY* 4.1 20.0 - - - +
668A LEU* 3.6 37.5 - - + +
672A CYS* 4.6 8.7 - - - -
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Residues in contact with GLY 122 (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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76A THR* 4.9 7.6 - - - -
118A SER 3.3 6.3 + - - -
119A LEU 3.2 11.4 + - - -
120A LEU 3.3 0.4 - - - -
121A ILE* 1.3 79.2 - - - +
123A LYS* 1.4 58.0 + - - +
652A ARG* 3.5 16.1 - - - +
655A MET* 5.0 5.7 - - - +
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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