Contacts of the helix formed by residues 75 - 87 (chain A) in PDB entry 1RMV
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 VAL 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A SER 3.4 0.2 - - - -
74A ALA* 1.3 79.6 - - - +
76A ILE* 1.3 77.2 - - - +
77A LYS 3.6 0.4 - - - -
78A PRO* 3.7 2.0 - - - -
79A LEU* 3.1 38.1 + - + +
128A LEU* 5.3 2.8 - - + +
131A GLU* 3.0 54.3 - - + +
132A LEU* 4.1 2.9 - - + +
136A HIS* 3.6 38.8 + - + +
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A MET* 4.1 23.3 - - - -
48A PHE* 4.2 7.9 - - + -
69A VAL* 5.8 2.5 - - + -
70A TYR 3.5 8.3 - - - +
71A VAL* 3.7 23.3 - - + +
73A SER* 3.1 37.9 - - - +
75A VAL* 1.3 84.9 - - + +
77A LYS* 1.3 60.6 + - - +
80A TYR* 2.5 57.5 + - + +
128A LEU* 3.8 22.2 - - + -
132A LEU* 4.5 7.2 - - + -
136A HIS 5.1 1.8 - - - +
137A GLY* 4.4 6.5 - - - -
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL 3.9 1.1 - - - +
72A ASN* 3.3 43.5 - - + +
73A SER 3.5 0.9 - - - +
76A ILE* 1.3 80.3 - - - +
78A PRO* 1.4 90.4 - - + +
80A TYR* 3.3 16.0 - - + -
81A GLU* 3.1 33.8 + - + +
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Residues in contact with PRO 78 (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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73A SER 3.4 11.4 - - - +
74A ALA 3.5 17.3 - - - +
75A VAL* 3.6 5.8 - - - +
77A LYS* 1.4 119.5 - - + +
79A LEU* 1.3 61.5 + - + +
81A GLU* 4.4 3.2 - - + +
82A ALA* 3.0 26.5 + - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.1 30.8 + - + +
76A ILE 3.4 0.2 - - - -
78A PRO* 1.3 83.0 - - + +
80A TYR* 1.3 52.3 + - - +
82A ALA* 3.9 7.9 - - + -
83A LEU* 2.8 36.6 + - - +
124A GLN* 3.3 44.3 - - + +
127A LEU* 5.4 10.3 - - + -
128A LEU* 3.9 15.7 - - + +
131A GLU* 5.6 6.1 - - + -
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Residues in contact with TYR 80 (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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15A ALA 5.5 2.3 + - - -
48A PHE* 3.4 35.0 - + + -
52A LEU* 3.5 35.6 - - + +
71A VAL* 3.2 21.5 - - + -
72A ASN* 5.7 0.4 - - + -
76A ILE* 2.5 42.5 + - + +
77A LYS* 3.3 35.9 - - + -
79A LEU* 1.3 73.2 - - - +
81A GLU* 1.3 68.9 + - + +
83A LEU* 3.7 4.9 - - - -
84A MET* 3.0 31.3 + - + +
128A LEU* 4.3 5.6 - - + -
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Residues in contact with GLU 81 (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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77A LYS* 3.1 22.0 + - + +
78A PRO* 4.4 3.4 - - + +
80A TYR* 1.3 86.4 - - + +
82A ALA* 1.3 61.1 + - - +
84A MET* 4.2 3.2 - - - +
85A LYS* 2.8 70.0 + - - +
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Residues in contact with ALA 82 (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 3.0 22.9 + - - +
79A LEU* 3.9 15.3 - - + +
81A GLU* 1.3 85.2 + - - +
83A LEU* 1.3 55.5 + - - +
85A LYS* 3.6 5.2 - - - +
86A SER* 3.0 28.5 + - - -
124A GLN* 5.3 4.0 - - + +
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Residues in contact with LEU 83 (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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27A CYS* 5.9 2.7 - - - -
48A PHE* 6.0 1.8 - - + -
79A LEU 2.8 23.9 + - - +
80A TYR* 3.9 2.2 - - - +
81A GLU 3.2 0.2 - - - -
82A ALA* 1.3 71.5 - - - +
84A MET* 1.3 86.4 + - + +
85A LYS 2.9 4.0 - - - -
86A SER* 2.7 34.6 + - - -
87A PHE* 4.0 6.7 - - + -
121A ILE* 3.2 44.2 - - + +
124A GLN* 3.6 20.6 - - + +
125A ILE* 3.7 23.3 - - + +
128A LEU* 3.7 22.0 - - + -
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Residues in contact with MET 84 (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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26A GLN* 4.0 4.7 - - - +
27A CYS* 6.5 0.4 - - - -
44A VAL* 3.5 23.6 - - + +
45A ARG* 3.1 54.7 - - + +
48A PHE* 3.6 43.1 - - + -
52A LEU* 6.4 0.4 - - - -
80A TYR* 3.0 27.9 + - + +
81A GLU* 4.2 3.8 - - - +
83A LEU* 1.3 86.8 - - + +
85A LYS* 1.3 57.0 + - - +
87A PHE* 3.1 43.3 - - + -
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Residues in contact with LYS 85 (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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45A ARG* 3.5 20.5 - - - +
81A GLU* 2.8 40.3 + - - +
82A ALA* 3.6 6.5 - - - +
84A MET* 1.3 74.4 - - - +
86A SER* 1.3 56.0 + - - +
87A PHE 3.0 3.4 - - - -
88A ASP* 2.6 68.4 + - + +
167B A 5.6 0.2 + - - -
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Residues in contact with SER 86 (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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41A ARG* 4.8 0.2 + - - -
82A ALA 3.0 16.4 + - - -
83A LEU* 2.7 22.3 + - - -
85A LYS* 1.3 69.8 - - - +
87A PHE* 1.3 55.1 + - - -
88A ASP 3.3 3.6 + - - -
89A THR 4.9 0.5 + - - +
117A ALA* 4.3 13.0 - - - +
120A ALA* 3.3 22.3 + - - +
121A ILE* 3.3 29.7 + - - -
124A GLN* 5.0 1.9 - - - +
167B A 3.9 24.4 + - - +
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Residues in contact with PHE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 2.9 73.5 - - + +
42A ASP* 5.3 0.2 - - - +
44A VAL* 3.7 10.5 - - + -
45A ARG* 3.0 31.9 + - + -
83A LEU* 4.0 4.7 - - + -
84A MET* 3.1 54.5 - - + -
85A LYS 2.8 0.8 + - - -
86A SER* 1.3 75.2 - - - +
88A ASP* 1.3 66.8 + - - +
89A THR 3.3 2.2 - - - -
117A ALA* 5.8 0.2 - - - -
121A ILE* 3.3 45.1 - - + -
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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