Contacts of the helix formed by residues 93 - 108 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C VAL 3.6 3.6 + - - -
92C THR* 1.3 69.6 - - - +
94C TYR* 1.3 63.1 + - - +
95C GLU* 3.5 18.2 - - - +
96C TYR* 3.1 35.3 + - + +
97C GLU* 3.1 23.7 + - - +
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Residues in contact with TYR 94 (chain C).
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* 5.0 7.2 - - + -
92C THR* 3.1 16.4 + - - +
93C ASP* 1.3 72.2 + - - +
95C GLU* 1.3 77.1 + - + +
97C GLU* 3.3 4.1 + - + +
98C LEU* 3.0 52.5 + - + +
88F LEU* 3.6 34.0 - - + +
89F ARG 2.7 29.5 + - - -
90F ALA* 4.9 6.3 - - - -
92F THR* 3.7 13.7 - - - -
94F TYR* 3.8 50.7 - + + -
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ALA* 3.2 29.6 - - + +
91A VAL* 3.8 20.6 - - + +
92A THR 5.9 0.7 - - - +
124A PHE* 6.2 1.1 - - + -
95B GLU* 4.9 8.1 - - - +
93C ASP* 3.5 12.5 - - - +
94C TYR* 1.3 95.4 + - + +
96C TYR* 1.3 60.3 + - - +
98C LEU* 3.8 8.4 - - + +
99C GLN* 2.8 31.4 + - - +
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Residues in contact with TYR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASN* 3.4 23.3 + - - -
39C ARG* 3.9 22.2 + - - -
86C ARG* 4.4 0.2 - - - -
93C ASP* 3.1 38.9 + - + +
95C GLU* 1.3 76.9 - - - +
97C GLU* 1.3 79.4 + - - +
99C GLN* 3.3 17.7 + - - +
100C MET* 2.8 69.4 + - + +
200C PNS 3.7 17.0 + - - -
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Residues in contact with GLU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ARG* 2.9 44.1 + - - +
87C GLY 4.5 6.9 - - - +
88C LEU* 4.1 9.2 - - + -
92C THR* 3.5 32.1 - - + +
93C ASP 3.1 8.5 + - - +
94C TYR* 3.3 10.3 + - + +
96C TYR* 1.3 85.8 - - + +
98C LEU* 1.4 58.4 + - + +
100C MET* 3.4 7.5 + - - +
101C ALA* 2.9 30.6 + - - +
115C PHE* 3.5 27.6 - - + -
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 4.2 21.1 - - + -
94C TYR* 3.0 55.6 + - + +
95C GLU* 3.8 9.0 - - + +
97C GLU* 1.4 74.6 - - + +
99C GLN* 1.3 65.1 + - - +
101C ALA* 3.3 4.7 + - - +
102C LEU* 2.9 33.4 + - + +
115C PHE* 5.5 0.2 - - + -
88F LEU* 4.5 1.6 - - + -
89F ARG* 4.1 2.5 - - - -
90F ALA* 4.0 29.8 - - - +
117F ILE* 3.3 38.1 - - + -
123F SER* 4.5 2.9 - - - +
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Residues in contact with GLN 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A VAL* 3.9 21.8 - - + +
124A PHE* 3.1 40.1 - - - +
126A SER* 3.8 18.6 + - - -
129A LEU* 4.0 21.7 - - + +
39C ARG* 5.0 8.5 - - - +
95C GLU 2.8 20.8 + - - +
96C TYR* 3.5 22.8 + - - +
98C LEU* 1.3 74.3 - - - +
100C MET* 1.3 58.3 + - + +
102C LEU* 3.4 1.4 + - - +
103C ALA* 2.8 30.5 + - - +
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Residues in contact with MET 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 5.9 1.1 - - + -
132A GLU* 5.0 0.4 - - - +
39C ARG* 4.7 9.0 - - - +
86C ARG* 4.8 7.6 - - - -
96C TYR* 2.8 67.3 + - + +
97C GLU* 3.7 8.5 - - - +
99C GLN* 1.3 76.5 - - + +
101C ALA* 1.3 58.4 + - - +
103C ALA* 3.7 5.3 - - - +
104C ASN* 2.8 50.2 + - - +
200C PNS 3.0 59.2 - - - +
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C GLU 2.9 18.1 + - - +
98C LEU 3.6 4.3 - - - +
100C MET* 1.3 77.3 - - - +
102C LEU* 1.3 57.4 + - - +
104C ASN* 3.8 4.2 - - - +
105C LYS* 3.0 29.8 + - - +
111C LEU* 5.1 0.3 - - - +
113C THR* 4.1 30.0 + - + -
115C PHE* 4.5 1.3 - - + -
117F ILE* 3.7 28.9 - - + -
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 3.6 49.8 - - + -
98C LEU* 2.9 21.7 + - + +
99C GLN* 3.9 3.1 - - - +
101C ALA* 1.3 73.4 - - - +
103C ALA* 1.3 65.9 + - - +
105C LYS* 3.5 9.4 + - + +
106C LYS* 3.1 27.5 + - - +
117F ILE* 3.9 16.8 - - + +
118F ALA 3.4 23.8 - - - +
119F SER* 4.0 4.3 - - - -
120F GLU* 3.8 32.7 - - + +
123F SER* 5.4 0.2 - - - +
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 3.9 34.3 - - + -
143A TRP* 4.2 17.0 - - + -
99C GLN 2.8 18.7 + - - +
100C MET 3.7 3.4 - - - +
102C LEU* 1.3 72.1 - - - +
104C ASN* 1.3 65.8 + - - +
106C LYS* 3.0 4.9 + - - +
107C LEU* 3.0 27.7 + - + +
200C PNS 4.0 9.6 - - - -
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Residues in contact with ASN 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 5.7 0.2 - - - +
72C LEU* 4.2 11.3 - - - +
73C VAL* 3.7 19.7 - - + +
84C LEU* 4.0 17.7 - - + +
100C MET* 2.8 35.5 + - - +
101C ALA* 3.8 4.9 - - - +
103C ALA* 1.3 74.0 - - - +
105C LYS* 1.3 55.9 + - - +
107C LEU* 3.2 7.9 + - - +
108C TYR* 2.8 32.7 + - - +
111C LEU* 3.4 20.9 - - + -
200C PNS 3.3 28.6 + - - +
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Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ALA 3.0 19.2 + - - +
102C LEU* 3.8 10.3 - - + +
103C ALA 3.2 0.2 - - - -
104C ASN* 1.3 73.7 - - - +
106C LYS* 1.3 65.9 + - - +
108C TYR 3.0 24.2 - - - +
109C SER* 3.2 34.6 + - - +
110C ASP 4.4 2.0 + - - -
111C LEU* 2.5 35.5 + - + +
112C GLU* 2.8 22.2 + - - +
22F ARG* 4.1 25.1 - - - +
119F SER* 6.5 1.3 - - - -
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Residues in contact with LYS 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LYS* 4.0 18.6 + - - +
125A ILE* 4.4 5.7 - - - +
142A GLU* 3.1 41.4 - - + +
143A TRP* 3.2 36.6 - - + +
102C LEU 3.1 10.8 + - - +
103C ALA* 3.0 11.5 + - - +
105C LYS* 1.3 78.7 - - - +
107C LEU* 1.3 61.5 + - + +
108C TYR 3.5 0.2 + - - -
109C SER* 4.7 4.2 + - - -
120F GLU* 3.1 33.2 + - - +
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A VAL* 3.8 33.2 - - + -
138A GLY* 5.0 1.3 - - - -
139A ASP* 3.5 33.4 - - + +
143A TRP* 4.4 10.5 - - + -
71C LEU* 4.1 21.1 - - + -
73C VAL* 3.8 15.3 - - + -
77C LYS* 2.8 31.5 + - - +
103C ALA 3.0 18.6 + - - +
104C ASN* 3.2 12.8 + - - +
106C LYS* 1.3 79.2 - - + +
108C TYR* 1.3 53.8 + - - +
109C SER 4.1 0.4 - - - -
200C PNS 5.2 1.1 - - - -
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Residues in contact with TYR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C VAL* 3.9 21.8 - - + -
76C LEU* 3.8 16.5 + - + -
77C LYS* 3.7 34.5 - - + +
80C GLY* 4.6 2.9 - - - -
81C ILE 2.8 33.7 + - - -
82C LYS* 3.7 16.1 - - - +
104C ASN 2.8 10.8 + - - +
105C LYS* 3.0 8.8 - - - +
107C LEU* 1.3 79.8 - - - +
109C SER* 1.3 62.1 + - - +
110C ASP* 4.0 22.9 - - + -
111C LEU* 3.0 48.8 + - + +
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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