Contacts of the helix formed by residues 112 - 129 (chain A) in PDB entry 1VI7
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 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 5.7 0.4 - - - +
111A LEU* 1.3 82.7 - - - +
113A THR* 1.3 66.0 + - - -
114A GLY 3.3 3.4 - - - -
115A GLY* 3.7 5.4 - - - +
116A LEU* 3.2 19.3 + - - +
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Residues in contact with THR 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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78A PRO* 5.9 5.1 - - - +
81A THR* 3.3 21.7 + - - -
112A GLY* 1.3 68.8 - - - -
114A GLY* 1.3 72.0 + - - +
116A LEU* 3.2 6.9 + - - +
117A VAL* 3.2 19.5 + - - +
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLY* 3.3 0.6 - - - -
113A THR* 1.3 83.5 - - - +
115A GLY* 1.3 61.8 + - - +
117A VAL* 2.9 19.7 + - - +
118A LYS* 3.0 32.2 + - - +
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 4.9 1.6 - - - +
111A LEU* 3.4 32.4 - - - +
112A GLY* 3.4 11.2 + - - -
113A THR 3.3 0.8 - - - -
114A GLY* 1.3 75.1 - - - +
116A LEU* 1.3 58.6 + - - +
118A LYS* 3.7 6.6 + - - +
119A ALA* 3.4 17.3 + - - +
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Residues in contact with LEU 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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25A PHE* 5.1 3.4 - - + -
77A GLU* 3.9 11.2 - - - +
78A PRO* 3.3 39.7 - - + -
81A THR* 3.4 22.2 - - + +
104A ARG* 3.8 31.2 - - - +
111A LEU* 4.0 19.1 - - + +
112A GLY 3.2 15.2 + - - +
113A THR* 3.6 5.2 - - - +
114A GLY 3.2 0.6 - - - -
115A GLY* 1.3 73.3 - - - +
117A VAL* 1.3 61.9 + - - +
119A ALA* 3.1 3.0 + - - +
120A TYR* 2.9 41.5 + - + -
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY 4.6 2.7 - - - +
81A THR* 3.3 36.3 - - - +
85A PRO* 4.1 19.3 - - + -
113A THR* 3.2 8.5 + - - +
114A GLY* 2.9 11.5 + - - +
116A LEU* 1.3 76.3 - - - +
118A LYS* 1.3 68.3 + - + +
121A GLY* 2.8 30.5 + - - +
122A GLY 3.7 0.3 + - - -
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Residues in contact with LYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 5.1 2.9 - - - +
20A ILE* 4.8 5.4 - - + +
114A GLY* 3.0 27.5 + - - +
115A GLY* 3.7 6.0 + - - +
116A LEU 3.3 0.2 - - - -
117A VAL* 1.3 85.4 - - + +
119A ALA* 1.3 59.7 + - - +
120A TYR 3.4 0.2 - - - -
122A GLY* 3.3 23.2 - - - +
123A GLY 4.0 0.7 + - - -
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Residues in contact with ALA 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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18A GLU* 5.1 3.0 - - - +
20A ILE* 3.5 27.1 - - + -
25A PHE* 3.7 35.4 - - + +
102A VAL* 4.2 10.2 - - - +
111A LEU* 5.2 0.2 - - + -
115A GLY 3.4 14.2 + - - +
116A LEU* 3.1 7.9 + - - +
118A LYS* 1.3 78.9 - - - +
120A TYR* 1.3 63.0 + - + +
123A GLY* 3.4 17.5 + - - -
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Residues in contact with TYR 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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25A PHE* 4.1 15.7 - + - -
54A HIS* 4.0 0.2 - - - +
56A CYS* 3.2 25.4 - - - -
77A GLU* 3.1 33.0 + - + +
81A THR 3.7 5.6 - - - +
82A ALA* 3.5 28.3 - - + +
85A PRO* 5.0 2.0 - - + -
86A MET* 3.2 30.0 - - + +
102A VAL* 3.5 28.7 - - + +
104A ARG* 3.5 19.5 - - + +
116A LEU* 2.9 33.3 + - + +
119A ALA* 1.3 80.0 - - + +
121A GLY* 1.3 70.1 + - - +
123A GLY* 3.2 1.0 + - - -
124A VAL* 3.1 25.3 + - - +
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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
----------------------------------------------------------
85A PRO* 3.9 32.2 - - - +
86A MET* 4.0 1.1 - - - -
89A GLN* 3.5 17.9 - - - +
117A VAL* 2.8 17.0 + - - -
120A TYR* 1.3 71.4 - - - +
122A GLY* 1.3 62.7 + - - +
124A VAL* 2.9 5.0 + - - -
125A ASN* 2.9 18.2 + - - -
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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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18A GLU* 5.2 2.0 - - - -
117A VAL 3.7 3.2 + - - -
118A LYS* 3.3 21.6 + - - +
120A TYR 3.3 0.2 - - - -
121A GLY* 1.3 75.6 - - - +
123A GLY* 1.3 59.0 + - - +
125A ASN* 3.2 11.8 + - - +
126A GLN* 3.0 30.9 + - - +
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Residues in contact with GLY 123 (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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16A VAL* 4.9 0.7 - - - +
18A GLU* 4.8 9.6 + - - -
25A PHE* 6.5 0.2 - - - -
27A THR* 3.4 25.9 + - - -
102A VAL* 5.3 0.4 - - - -
118A LYS 4.0 0.4 + - - -
119A ALA 3.4 19.0 + - - -
120A TYR 3.2 4.7 + - - -
122A GLY* 1.3 73.4 - - - +
124A VAL* 1.3 62.9 + - - +
126A GLN* 3.1 14.8 + - - +
127A ALA* 3.3 12.1 + - - +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 4.0 17.3 - - + -
29A LEU* 4.6 3.1 - - + -
86A MET* 3.2 42.0 - - + +
89A GLN* 3.9 9.2 - - + -
90A LEU* 3.5 32.1 - - + -
100A ALA* 4.1 11.0 - - + -
102A VAL* 4.2 1.3 - - + -
120A TYR 3.1 5.1 + - - +
121A GLY 2.9 7.6 + - - +
123A GLY* 1.3 74.7 - - - +
125A ASN* 1.3 62.9 + - - +
126A GLN 3.3 0.2 + - - -
127A ALA* 3.6 1.6 - - - +
128A LEU* 3.0 40.3 + - + +
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Residues in contact with ASN 125 (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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89A GLN* 2.6 32.2 + - - +
121A GLY 2.9 9.7 + - - +
122A GLY* 3.2 17.3 - - - +
124A VAL* 1.3 78.5 - - - +
126A GLN* 1.3 66.1 + - - +
128A LEU* 3.5 8.3 + - - +
129A ARG* 3.1 48.8 + - - +
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Residues in contact with GLN 126 (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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16A VAL* 4.4 16.6 - - + -
18A GLU* 4.8 13.0 - - - +
122A GLY* 3.0 19.4 + - - +
123A GLY* 3.1 6.5 + - - +
125A ASN* 1.3 82.6 - - - +
127A ALA* 1.3 67.1 + - - +
129A ARG* 3.1 50.8 + - - +
130A GLN* 3.7 13.1 + - - +
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Residues in contact with ALA 127 (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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14A VAL* 3.6 12.8 - - + +
16A VAL* 3.4 26.0 - - + +
27A THR* 4.0 6.1 - - + +
29A LEU* 3.4 33.7 - - + -
123A GLY 3.3 7.7 + - - +
124A VAL 3.6 5.2 - - - +
126A GLN* 1.3 78.5 - - - +
128A LEU* 1.3 56.2 + - - +
130A GLN* 2.8 24.2 + - - +
131A LEU* 3.3 9.9 + - - +
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Residues in contact with LEU 128 (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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29A LEU* 3.4 24.5 - - + -
89A GLN* 3.8 31.2 - - + +
90A LEU* 4.3 6.1 - - + -
93A SER* 4.3 19.5 - - - +
98A ILE* 4.2 8.1 - - + -
124A VAL* 3.0 39.0 + - + +
125A ASN* 3.6 8.3 - - - +
127A ALA* 1.3 79.1 - - - +
129A ARG* 1.3 59.8 + - - +
130A GLN 3.2 1.0 + - - -
131A LEU* 3.3 32.1 + - + +
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Residues in contact with ARG 129 (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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125A ASN* 3.1 31.4 + - - +
126A GLN* 3.1 41.9 + - - +
128A LEU* 1.3 75.6 - - - +
130A GLN* 1.3 61.2 + - + +
131A LEU 3.5 0.8 - - - +
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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