Contacts of the helix formed by residues 93 - 108 (chain F) in PDB entry 1VLH
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 ASP 93 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91F VAL 3.6 3.2 + - - -
92F THR* 1.3 71.3 - - - +
94F TYR* 1.3 63.4 + - - +
95F GLU* 3.5 14.1 + - - +
96F TYR* 3.3 41.0 + - + +
97F GLU* 3.1 24.1 + - - +
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Residues in contact with TYR 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU* 3.3 33.5 - - + +
89C ARG 2.8 29.6 + - - -
90C ALA* 4.9 5.6 - - - -
92C THR* 3.7 11.9 - - - -
94C TYR* 3.8 60.3 - + + -
88F LEU* 5.1 5.8 - - + -
92F THR* 3.1 12.2 + - - +
93F ASP* 1.3 72.8 + - - +
95F GLU* 1.3 80.4 + - + +
97F GLU* 3.3 5.8 + - + +
98F LEU* 3.0 52.8 + - + +
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Residues in contact with GLU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ALA* 3.3 27.6 - - + +
91D VAL* 3.6 20.9 - - + +
92D THR 5.9 0.4 - - - +
124D PHE* 6.3 0.7 - - + -
95E GLU* 5.5 2.9 - - - +
93F ASP* 3.5 12.7 - - - +
94F TYR* 1.3 97.8 + - + +
96F TYR* 1.3 60.1 + - - +
98F LEU* 3.9 9.8 - - + +
99F GLN* 3.0 29.1 + - - +
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Residues in contact with TYR 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F ASN* 3.8 10.0 + - - -
39F ARG* 4.2 21.9 + - - -
86F ARG* 4.3 3.4 - - - -
92F THR* 6.1 0.2 - - + -
93F ASP* 3.3 39.3 + - + +
95F GLU* 1.3 76.3 - - - +
97F GLU* 1.3 78.4 + - + +
99F GLN* 3.4 15.8 + - - +
100F MET* 3.0 66.6 + - + +
200F PNS 3.7 27.8 + - - +
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Residues in contact with GLU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ARG* 2.8 47.1 + - - +
87F GLY 4.8 4.9 - - - +
88F LEU* 4.2 5.2 - - + -
92F THR* 3.6 30.8 - - + +
93F ASP 3.1 8.6 + - - +
94F TYR* 3.5 10.1 - - + +
96F TYR* 1.3 84.5 - - + +
98F LEU* 1.3 58.9 + - + +
100F MET* 3.5 10.4 + - - +
101F ALA* 2.9 30.1 + - - +
115F PHE* 3.5 31.2 - - + -
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Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU* 4.5 3.6 - - + +
89C ARG 4.1 1.8 - - - -
90C ALA* 4.0 28.0 - - - +
117C ILE* 3.2 38.8 - - + -
123C SER* 4.6 2.5 - - - +
124D PHE* 4.3 19.5 - - + -
94F TYR* 3.0 55.7 + - + +
95F GLU* 4.0 8.7 - - + +
97F GLU* 1.3 74.3 - - + +
99F GLN* 1.3 68.0 + - - +
101F ALA* 3.3 4.3 + - - +
102F LEU* 2.9 33.0 + - + +
115F PHE* 5.7 0.2 - - + -
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Residues in contact with GLN 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D VAL* 3.9 21.6 - - + +
124D PHE* 2.9 44.5 + - - +
125D ILE* 4.0 3.2 - - - +
126D SER* 3.4 24.0 + - - -
129D LEU* 4.0 20.1 - - + +
39F ARG* 5.5 5.9 + - - -
95F GLU 3.0 20.0 + - - +
96F TYR* 3.5 17.6 - - - +
97F GLU 3.4 0.2 - - - -
98F LEU* 1.3 77.4 - - - +
100F MET* 1.3 54.5 + - - +
102F LEU* 3.7 1.7 - - - +
103F ALA* 2.8 33.4 + - - +
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Residues in contact with MET 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LEU* 5.7 0.4 - - + -
132D GLU* 5.7 0.9 - - - +
39F ARG* 5.7 1.8 - - - -
86F ARG* 3.4 34.5 - - - +
96F TYR* 3.0 49.7 + - + +
97F GLU* 3.6 15.9 - - - +
98F LEU 3.2 0.2 - - - -
99F GLN* 1.3 78.8 - - + +
101F ALA* 1.3 59.7 + - - +
103F ALA* 3.9 0.6 - - - +
104F ASN* 2.9 43.8 + - - +
200F PNS 3.7 49.6 - - + +
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Residues in contact with ALA 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ILE* 3.7 30.3 - - + -
97F GLU 2.9 18.4 + - - +
98F LEU 3.7 2.0 - - - +
100F MET* 1.3 77.8 - - - +
102F LEU* 1.3 57.3 + - - +
104F ASN* 3.5 4.0 + - - +
105F LYS* 3.0 30.4 + - - +
111F LEU* 4.8 0.7 - - - +
113F THR* 4.1 31.7 + - + -
115F PHE* 4.4 1.1 - - + -
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Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C ILE* 3.9 17.9 - - + +
118C ALA 3.6 21.1 - - - +
119C SER* 3.9 4.9 - - - -
120C GLU* 3.6 40.2 - - + +
123C SER* 5.4 0.9 - - - +
124D PHE* 3.7 44.4 - - + -
98F LEU* 2.9 22.4 + - + +
99F GLN* 3.8 4.3 - - - +
101F ALA* 1.3 72.8 - - - +
103F ALA* 1.3 66.2 + - - +
105F LYS* 3.4 11.6 + - + +
106F LYS* 3.0 22.9 + - - +
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Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LEU* 3.8 36.6 - - + -
143D TRP* 4.2 15.6 - - + -
99F GLN 2.8 22.0 + - - +
100F MET 3.9 3.6 - - - +
102F LEU* 1.3 72.0 - - - +
104F ASN* 1.3 65.5 + - - +
106F LYS* 3.3 4.3 + - - +
107F LEU* 3.0 28.1 + - + +
200F PNS 4.0 7.4 - - - -
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Residues in contact with ASN 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F LEU* 5.6 0.2 - - - +
72F LEU* 4.1 13.0 - - - +
73F VAL* 3.7 19.5 + - + +
84F LEU* 3.8 17.6 - - - +
100F MET* 2.9 34.0 + - - +
101F ALA* 3.9 3.9 - - - +
103F ALA* 1.3 76.0 - - - +
105F LYS* 1.3 58.1 + - - +
107F LEU* 3.3 9.5 + - - +
108F TYR* 2.9 33.1 + - - +
111F LEU* 3.4 19.1 - - + -
200F PNS 3.4 25.1 - - - +
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Residues in contact with LYS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 4.5 20.4 - - - +
101F ALA 3.0 19.1 + - - +
102F LEU* 3.7 13.2 - - + +
103F ALA 3.2 0.2 - - - -
104F ASN* 1.3 73.4 - - - +
106F LYS* 1.3 65.2 + - - +
108F TYR 3.2 20.9 - - - +
109F SER* 2.8 38.3 + - - +
110F ASP 4.6 1.4 - - - -
111F LEU* 3.2 29.4 + - + +
112F GLU* 3.4 16.9 + - - -
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Residues in contact with LYS 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C GLU* 5.5 6.3 - - - +
142D GLU* 5.1 17.7 - - + -
143D TRP* 4.1 27.4 - - + +
102F LEU 3.0 13.9 + - - +
103F ALA* 3.3 12.8 - - - +
105F LYS* 1.3 78.9 - - - +
107F LEU* 1.3 61.1 + - + +
108F TYR 3.5 0.3 + - - -
109F SER* 4.8 3.1 + - - -
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Residues in contact with LEU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D VAL* 4.1 31.2 - - + -
138D GLY* 4.8 2.5 - - - -
139D ASP* 3.5 34.8 - - + +
143D TRP* 4.4 9.6 - - + -
71F LEU* 4.2 20.2 - - + -
73F VAL* 3.8 14.4 - - + -
77F LYS* 3.1 24.6 + - - +
103F ALA 3.0 19.8 + - - +
104F ASN* 3.5 21.5 - - - +
106F LYS* 1.3 76.9 - - + +
108F TYR* 1.3 57.1 + - - +
109F SER 4.1 0.4 - - - -
200F PNS 5.1 1.3 - - - -
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Residues in contact with TYR 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F VAL* 3.8 20.4 - - + -
76F LEU* 3.8 19.3 + - + -
77F LYS* 3.8 34.9 - - + +
80F GLY* 4.7 1.9 - - - -
81F ILE 2.8 32.9 + - - -
82F LYS* 3.7 21.3 - - + -
104F ASN 2.9 11.4 + - - +
105F LYS* 3.2 7.5 - - - +
106F LYS 3.3 0.2 - - - -
107F LEU* 1.3 80.5 - - - +
109F SER* 1.3 61.7 + - - +
110F ASP* 4.0 18.2 - - + -
111F LEU* 3.0 44.4 + - + +
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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