Contacts of the helix formed by residues 142 - 154 (chain H) in PDB entry 1VQ9
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 142 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H LEU* 5.4 0.6 - - + +
77H LEU* 3.0 51.6 - - + +
82H ASP* 4.3 3.8 + - - +
138H CYS* 3.6 19.3 - - + +
139H ASN* 3.3 19.8 + - - +
141H GLU* 1.3 85.3 - - - +
143H ALA* 1.3 62.3 + - - +
144H GLU 3.3 1.8 - - - -
145H HIS* 3.1 25.0 + - + +
146H VAL* 3.2 10.9 + - - +
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Residues in contact with ALA 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H VAL* 4.7 12.8 - - + -
47H ILE* 4.0 3.9 - - + +
138H CYS* 3.6 15.5 - - - -
139H ASN 3.5 2.6 + - - +
140H VAL* 3.6 21.5 - - + +
141H GLU 2.9 3.8 + - - +
142H ASP* 1.3 76.4 - - - +
144H GLU* 1.3 68.4 + - + +
146H VAL* 2.8 23.6 - - - +
147H LYS* 3.3 13.7 + - - +
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Residues in contact with GLU 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H GLU 4.2 5.5 + - - +
142H ASP 3.3 0.2 - - - -
143H ALA* 1.3 80.4 - - + +
145H HIS* 1.3 67.3 + - + +
146H VAL 3.4 0.2 - - - -
147H LYS* 2.7 47.5 + - - +
148H GLU* 3.4 20.3 + - - +
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Residues in contact with HIS 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H HIS* 3.5 16.0 + - - -
73H LEU* 3.6 10.6 - - + +
76H GLU* 3.2 43.8 + - + +
77H LEU* 3.7 26.0 - - + -
141H GLU 5.0 2.7 - - - -
142H ASP* 3.1 28.8 + - + +
144H GLU* 1.3 82.0 + - + +
146H VAL* 1.3 63.6 + - - +
148H GLU* 3.5 2.8 + - - +
149H ALA 3.2 14.6 + - - -
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Residues in contact with VAL 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H ILE* 3.5 24.2 - - + -
73H LEU* 3.9 17.2 - - + +
136H ALA* 3.4 32.1 - - + -
138H CYS* 3.9 12.8 - - + -
142H ASP 3.2 8.4 + - - +
143H ALA* 2.8 30.5 - - - +
145H HIS* 1.3 74.9 - - - +
147H LYS* 1.3 64.3 + - - +
148H GLU 3.0 1.6 - - - -
149H ALA* 3.0 12.6 + - + +
150H PHE* 3.1 32.8 + - + -
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Residues in contact with LYS 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12210 G 5.7 2.8 + - - -
47H ILE* 4.1 23.6 - - + -
143H ALA* 3.3 12.9 + - - +
144H GLU* 2.7 44.2 + - - +
145H HIS 3.4 0.2 - - - -
146H VAL* 1.3 82.6 - - - +
148H GLU* 1.3 61.4 + - - +
150H PHE 3.7 0.2 + - - -
151H ARG* 3.3 17.8 + - - +
163H ILE* 3.6 36.5 - - + +
165H SER* 5.4 8.1 - - - -
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Residues in contact with GLU 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H HIS* 3.7 28.9 - - + +
144H GLU 3.4 16.1 + - - +
145H HIS* 3.8 1.6 - - - +
146H VAL 3.0 0.6 - - - -
147H LYS* 1.3 80.1 - - - +
149H ALA* 1.3 64.9 + - - +
150H PHE 3.2 0.4 - - - -
151H ARG* 3.2 54.2 + - - +
152H ARG* 3.2 24.5 + - - +
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Residues in contact with ALA 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H ALA* 3.2 41.7 - - + +
72H HIS* 3.9 13.2 - - + -
73H LEU* 3.9 17.3 - - + -
85H MET* 5.5 0.2 - - - -
145H HIS 3.2 14.4 + - - +
146H VAL* 3.0 9.4 + - - +
148H GLU* 1.3 77.6 - - - +
150H PHE* 1.3 61.5 + - + +
152H ARG* 3.6 3.3 + - - +
153H ALA 3.1 17.8 + - - -
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Residues in contact with PHE 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H ILE* 3.3 34.1 - - + -
48H SER 3.5 20.0 - - - -
49H LEU* 3.7 20.7 - - + +
69H ALA* 5.0 0.7 - - + -
85H MET* 3.7 26.5 - - - -
134H PHE* 4.1 19.1 - + + -
135H THR 4.4 0.4 - - - -
136H ALA* 3.9 10.5 - - + -
146H VAL* 3.1 29.9 + - + +
147H LYS 4.0 4.9 - - - +
148H GLU 3.2 0.2 - - - -
149H ALA* 1.3 80.8 - - + +
151H ARG* 1.3 57.2 + - - +
152H ARG 3.1 1.6 - - - -
153H ALA* 3.3 9.5 - - + +
154H TYR* 2.7 39.0 + - - +
163H ILE* 3.9 24.9 - - + -
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Residues in contact with ARG 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11350 G 4.4 8.7 - - - +
25020 C 3.1 15.9 + - - -
25030 A 2.4 32.1 + - - -
147H LYS 3.3 13.0 + - - +
148H GLU* 3.2 40.6 + - - +
150H PHE* 1.3 79.4 - - - +
152H ARG* 1.3 72.4 + - - +
154H TYR* 3.2 43.5 - - + +
155H ASN* 2.8 31.3 + - - +
163H ILE* 4.2 3.1 - - + +
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Residues in contact with ARG 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25020 C 4.2 13.5 + - - +
25030 A 3.9 29.8 + - - -
25040 A 2.9 34.3 + - - -
68H SER* 3.5 33.0 + - - +
72H HIS* 4.2 33.7 + - - +
75H LYS* 6.0 2.0 - - - +
148H GLU* 3.2 19.2 + - - +
149H ALA 3.9 7.6 - - - +
150H PHE 3.1 0.6 - - - -
151H ARG* 1.3 96.8 - - - +
153H ALA* 1.3 63.4 + - - +
155H ASN* 3.5 14.2 + - - +
156H LYS* 4.0 7.4 + - - +
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Residues in contact with ALA 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H LEU* 4.0 13.5 - - + -
65H SER* 3.4 35.3 - - - +
68H SER* 4.2 0.2 - - - -
69H ALA* 3.9 13.9 - - + -
134H PHE* 4.7 5.6 - - + -
149H ALA 3.1 15.2 + - - +
150H PHE* 2.9 15.6 + - + +
152H ARG* 1.3 73.6 - - - +
154H TYR* 1.3 58.5 + - - +
155H ASN 3.0 4.5 - - - -
156H LYS* 3.0 17.3 + - - -
157H ILE* 3.9 4.3 + - - +
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Residues in contact with TYR 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11340 G 3.9 18.6 - - - -
11350 G 3.1 31.9 + - - -
49H LEU* 3.9 17.4 - - + +
150H PHE 2.7 21.7 + - - +
151H ARG* 3.2 33.7 - - + +
153H ALA* 1.3 71.8 - - - +
155H ASN* 1.3 73.5 + - - +
156H LYS 3.1 2.1 + - - -
157H ILE* 3.6 14.2 - - - +
161H CYS* 3.6 39.0 - - + +
163H ILE* 3.8 18.9 - - + +
9486H SR 3.0 26.5 - - - -
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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