Contacts of the helix formed by residues 103 - 118 (chain C) in PDB entry 1VQM
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 ASN 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6560 G 3.7 3.6 - - - +
6570 G 3.7 12.5 + - - +
6630 C 3.6 31.6 + - - +
6640 U 3.5 8.1 - - - +
7490 C 2.7 48.1 + - - -
7500 A 3.1 14.3 + - - +
102C LEU* 1.3 78.3 - - - +
104C ASP* 1.3 64.9 + - - +
105C LYS 4.3 0.2 - - - +
106C GLU* 3.7 20.7 + - + +
107C ARG* 3.0 21.1 + - - +
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Residues in contact with ASP 104 (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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6640 U 2.8 44.0 + - - +
6800 G 4.3 7.1 - - - +
6810 G 5.2 2.1 - - - +
102C LEU 3.4 1.2 + - - +
103C ASN* 1.3 72.6 - - - +
105C LYS* 1.3 58.3 + - + +
107C ARG* 2.6 36.7 + - - +
108C GLN* 2.8 45.2 + - - +
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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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6570 G 3.6 13.2 - - - +
6580 C 3.4 25.9 + - - -
6620 U 3.4 27.5 + - - -
6630 C 2.7 38.7 + - - +
6640 U 5.0 2.1 + - - +
103C ASN* 3.2 1.0 - - - +
104C ASP* 1.3 77.0 - - + +
106C GLU* 1.3 59.3 + - - +
108C GLN* 3.3 11.9 + - - +
109C LEU* 2.9 30.7 + - - +
112C ARG* 5.2 2.0 + - - +
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Residues in contact with GLU 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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6560 G 3.0 40.8 + - - +
6570 G 3.3 35.6 + - - +
7500 A 5.1 1.0 - - - -
30C LEU* 4.0 15.6 - - + +
33C LYS* 3.0 33.3 + - + +
102C LEU* 4.1 16.0 - - + +
103C ASN* 3.3 20.4 + - + +
104C ASP 3.3 0.4 - - - -
105C LYS* 1.3 78.9 - - - +
107C ARG* 1.3 62.2 + - - +
109C LEU* 3.4 6.8 + - - +
110C ALA* 3.2 20.3 + - - +
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Residues in contact with ARG 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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6760 C 5.0 0.4 - - - -
6770 C 3.1 37.9 + - - +
6780 G 2.6 27.9 + - - -
34C ALA* 4.9 7.2 - - + -
102C LEU* 4.0 31.7 + - + +
103C ASN 3.0 11.9 + - - +
104C ASP* 2.6 47.0 + - - +
106C GLU* 1.3 77.5 - - - +
108C GLN* 1.3 75.8 + - - +
110C ALA* 3.1 9.1 + - - +
111C VAL* 3.1 22.9 + - + +
220C THR* 5.3 0.9 - - - +
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Residues in contact with GLN 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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6780 G 2.8 30.0 + - - +
6790 G 4.9 9.1 + - - -
104C ASP* 2.8 33.7 + - - +
105C LYS* 3.8 10.8 + - - +
107C ARG* 1.3 86.0 - - - +
109C LEU* 1.3 65.7 + - - +
111C VAL* 3.1 10.2 + - + +
112C ARG* 3.1 51.7 + - - +
246C ARG* 4.7 10.8 + - - +
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Residues in contact with LEU 109 (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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6570 G 3.9 26.7 - - - +
6580 C 4.0 9.0 - - - +
24C THR* 4.4 19.1 - - + -
25C PRO* 6.0 0.7 - - + +
27C ARG* 5.0 5.8 - - + +
30C LEU* 3.5 29.4 - - + -
105C LYS 2.9 17.6 + - - +
106C GLU* 3.6 5.6 - - - +
107C ARG 3.2 0.2 - - - -
108C GLN* 1.3 76.4 - - - +
110C ALA* 1.3 57.8 - - - +
112C ARG* 3.4 16.0 + - + +
113C SER* 2.9 28.5 + - - -
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Residues in contact with ALA 110 (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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30C LEU* 3.5 35.0 - - + +
31C ILE* 3.8 6.5 - - - +
34C ALA* 3.8 17.5 - - + -
106C GLU 3.2 9.6 + - - +
107C ARG 3.1 11.0 + - - +
109C LEU* 1.3 77.8 - - - +
111C VAL* 1.3 60.1 + - - +
113C SER* 3.3 7.2 + - - -
114C ALA* 2.8 30.0 + - - +
220C THR* 4.2 2.8 - - - +
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Residues in contact with VAL 111 (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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6770 C 4.4 14.1 - - - +
107C ARG* 3.1 15.5 + - + +
108C GLN* 3.1 11.8 + - + +
110C ALA* 1.3 77.0 - - - +
112C ARG* 1.3 58.4 + - + +
114C ALA* 3.1 5.4 + - - +
115C LEU* 2.8 36.2 + - + +
218C VAL* 4.2 17.9 - - + +
219C ASN* 4.8 2.0 - - - -
220C THR* 3.4 26.5 - - - +
223C LEU* 4.4 11.8 - - + +
246C ARG* 4.4 25.8 - - + +
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Residues in contact with ARG 112 (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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21C VAL* 3.9 18.6 - - + +
24C THR* 3.9 20.0 - - + +
105C LYS* 5.2 1.8 + - - +
108C GLN* 3.1 40.1 + - - +
109C LEU* 3.7 16.9 - - - +
111C VAL* 1.3 77.0 - - + +
113C SER* 1.3 57.7 + - - +
115C LEU* 3.2 12.4 + - + +
116C ALA* 2.9 29.3 + - - +
246C ARG* 2.7 45.9 + - + +
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Residues in contact with SER 113 (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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24C THR* 4.1 10.7 - - - +
25C PRO 3.2 10.3 + - - -
26C VAL* 3.4 2.9 - - - +
27C ARG* 2.5 41.4 + - - +
31C ILE* 3.8 9.3 - - - +
109C LEU* 2.9 20.2 + - - -
110C ALA* 3.6 8.5 - - - -
112C ARG* 1.3 79.3 - - - +
114C ALA* 1.3 61.9 + - - +
116C ALA* 3.4 5.0 + - - +
117C ALA* 3.1 21.0 + - - +
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Residues in contact with ALA 114 (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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31C ILE* 3.7 18.3 - - + +
110C ALA 2.8 17.7 + - - +
111C VAL* 3.1 4.9 + - - +
113C SER* 1.3 74.0 - - - +
115C LEU* 1.3 67.0 + - - +
117C ALA* 3.3 13.2 + - - +
118C THR* 3.5 12.8 + - - -
220C THR* 4.2 15.5 - - + -
223C LEU* 3.6 29.3 - - + +
224C ALA* 4.5 5.2 - - + -
229C PRO* 5.5 0.2 - - - -
230C GLY 5.1 0.5 + - - -
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Residues in contact with LEU 115 (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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21C VAL* 4.1 15.3 - - + -
22C PHE* 3.7 19.1 - - + -
111C VAL* 2.8 17.3 + - + +
112C ARG* 3.2 14.3 + - + +
114C ALA* 1.3 77.3 - - - +
116C ALA* 1.3 56.8 + - - +
118C THR* 3.0 27.3 + - - -
218C VAL* 5.1 2.7 - - + -
223C LEU* 3.9 25.3 - - + +
235C PHE* 3.8 28.3 - - + -
243C VAL* 3.3 44.0 - - + +
246C ARG* 4.9 9.4 - - + -
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Residues in contact with ALA 116 (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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21C VAL 3.6 13.0 + - - +
22C PHE* 3.6 21.9 - - - +
24C THR* 3.0 28.5 - - - +
26C VAL* 4.4 5.1 - - + +
112C ARG 2.9 16.4 + - - +
113C SER 3.6 5.8 - - - +
115C LEU* 1.3 72.7 - - - +
117C ALA* 1.3 60.1 + - - +
118C THR 3.0 5.8 - - - -
119C ALA* 3.1 17.7 + - - +
120C ASP* 4.1 4.2 + - - +
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Residues in contact with ALA 117 (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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26C VAL* 3.8 18.5 - - + +
113C SER 3.1 12.1 + - - +
114C ALA 3.7 8.5 - - - +
115C LEU 3.2 0.6 - - - -
116C ALA* 1.3 76.2 - - - +
118C THR* 1.3 61.0 + - - +
119C ALA 3.2 1.0 + - - -
120C ASP* 3.5 14.0 + - - +
123C LEU* 4.2 7.8 - - + +
124C VAL* 3.9 4.7 - - - +
229C PRO* 3.7 17.0 - - + -
230C GLY* 3.5 35.8 - - - +
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Residues in contact with THR 118 (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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22C PHE* 4.6 1.3 - - + -
114C ALA 3.5 10.6 + - - -
115C LEU* 3.0 15.5 + - - -
117C ALA* 1.3 79.2 - - - +
119C ALA* 1.3 56.3 + - - +
120C ASP 3.4 0.2 - - - -
124C VAL* 4.0 5.8 - - - +
136C VAL* 3.2 19.1 - - - +
137C PRO* 3.4 29.4 - - + +
223C LEU* 4.3 12.6 + - - +
230C GLY* 4.8 0.9 - - - -
231C ARG 3.7 16.3 + - - +
233C THR* 3.3 31.0 + - - +
235C PHE* 3.8 9.2 - - + -
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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