Contacts of the helix formed by residues 49 - 64 (chain A) in PDB entry 1V15
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 SER 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ARG 4.2 1.6 - - - -
6A ASN* 3.3 23.6 - - - -
8A PRO* 4.7 0.2 - - - -
48A LYS* 1.3 82.8 + - - +
50A PHE* 1.3 53.7 + - - +
51A ASP* 2.9 17.8 - - - +
52A ASP* 2.6 55.4 + - - +
53A PHE* 3.1 8.8 + - - +
114A TYR* 3.1 14.2 + - - -
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Residues in contact with PHE 50 (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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5A ARG* 3.3 64.0 + - + +
49A SER* 1.3 71.2 - - - +
51A ASP* 1.3 59.0 + - - +
52A ASP 3.1 0.2 - - - -
53A PHE* 3.7 26.5 - + - -
54A ARG* 3.2 33.1 + - + +
101A LEU* 3.9 38.1 - - + -
113A VAL* 3.5 42.2 - - + -
114A TYR* 3.0 11.7 + + - -
119A ILE* 4.1 10.8 - - + -
7E G 4.0 8.7 - - - -
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Residues in contact with ASP 51 (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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5A ARG* 4.4 4.0 + - - +
6A ASN* 3.9 21.0 + - - -
49A SER* 2.9 16.8 + - - +
50A PHE* 1.3 78.1 - - - +
52A ASP* 1.3 61.3 + - - +
54A ARG* 4.0 16.6 + - - +
55A LYS* 4.3 13.9 + - - +
8E C 2.8 39.9 + - - -
9F G 5.0 1.6 - - - +
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Residues in contact with ASP 52 (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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48A LYS* 3.4 38.9 - - + +
49A SER* 2.6 35.5 + - - +
51A ASP* 1.3 80.4 - - - +
53A PHE* 1.3 57.7 + - - +
54A ARG 3.4 0.7 - - - -
55A LYS* 3.8 8.9 - - - +
56A ALA* 3.2 27.2 + - - +
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Residues in contact with PHE 53 (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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11A ALA* 4.7 11.0 - - + -
49A SER 3.1 4.0 + - - +
50A PHE* 3.4 27.8 + + - +
52A ASP* 1.3 76.7 - - - +
54A ARG* 1.3 60.5 + - - +
55A LYS 3.4 0.2 - - - -
56A ALA* 3.5 7.7 + - + -
57A VAL* 2.9 52.3 + - + +
101A LEU* 5.1 4.0 - - + -
114A TYR* 3.8 33.9 - + + -
116A MET* 3.6 37.5 - - + -
119A ILE* 3.7 28.7 - - + -
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Residues in contact with ARG 54 (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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5A ARG* 5.2 5.5 - - - +
50A PHE* 3.2 29.5 + - + +
51A ASP* 4.0 27.4 + - - +
53A PHE* 1.3 75.4 - - - +
55A LYS* 1.3 66.9 + - - +
57A VAL* 3.2 6.8 + - - +
58A TRP* 3.0 46.1 + - + +
101A LEU* 3.5 24.2 - - + -
7E G 3.1 59.4 + - - -
8E C 2.9 43.0 + - - +
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Residues in contact with LYS 55 (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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51A ASP 4.3 12.1 + - - +
52A ASP* 3.8 11.6 + - - +
54A ARG* 1.3 79.0 - - - +
56A ALA* 1.3 52.9 + - - +
58A TRP 2.9 6.2 + - - -
59A GLU* 2.7 60.4 + - + +
81A LYS 3.3 14.4 + - - -
82A GLY* 3.6 25.7 - - - +
83A TYR* 5.0 14.1 + - - -
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Residues in contact with ALA 56 (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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52A ASP 3.2 15.9 + - - +
53A PHE* 3.6 9.9 - - + +
54A ARG 3.3 0.2 - - - -
55A LYS* 1.3 78.0 - - - +
57A VAL* 1.3 61.4 + - - +
59A GLU* 4.0 12.1 - - - +
60A GLU* 3.6 22.9 + - - +
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Residues in contact with VAL 57 (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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22A TRP* 6.1 1.8 - - + -
34A ILE* 5.6 14.8 - - + -
53A PHE* 2.9 47.0 + - + +
54A ARG* 3.4 12.3 - - - +
55A LYS 3.1 0.2 - - - -
56A ALA* 1.3 76.1 - - - +
58A TRP* 1.3 78.3 - - + +
59A GLU 3.2 0.9 - - - -
60A GLU* 3.1 20.8 + - - +
61A VAL* 3.2 18.4 + - + +
101A LEU* 5.2 12.3 - - + -
116A MET* 5.2 5.2 - - - -
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Residues in contact with TRP 58 (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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22A TRP* 3.9 31.9 - + - -
23A LEU* 4.4 6.5 - - + -
54A ARG* 3.0 43.1 + - + +
55A LYS 2.9 4.6 + - - -
57A VAL* 1.3 79.3 - - + +
59A GLU* 1.3 58.2 + - - +
60A GLU 3.3 0.4 - - - -
61A VAL* 3.5 31.9 + - + -
62A SER 3.6 0.3 + - - -
79A VAL* 2.7 36.8 - - + +
82A GLY 3.1 23.3 - - - +
83A TYR 3.5 9.4 - - - +
84A SER* 3.7 24.1 - - - -
85A PRO* 3.8 23.6 - - + -
99A TYR* 3.8 33.8 + + + -
101A LEU* 4.4 19.4 - - + +
121A VAL* 4.5 7.9 - - + -
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Residues in contact with GLU 59 (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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55A LYS* 2.7 55.4 + - - +
56A ALA* 4.2 9.7 - - - +
58A TRP* 1.3 74.7 - - - +
60A GLU* 1.3 61.0 + - + +
61A VAL 3.3 0.2 - - - -
62A SER* 2.5 22.1 + - - -
63A LYS* 3.2 27.6 + - - +
79A VAL 3.5 4.7 - - - +
80A SER 4.3 7.1 - - - +
81A LYS 3.7 7.7 - - - +
82A GLY* 3.6 17.3 - - - +
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Residues in contact with GLU 60 (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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56A ALA 3.6 14.1 + - - +
57A VAL* 3.1 10.1 + - - +
59A GLU* 1.3 77.1 - - + +
61A VAL* 1.3 59.8 + - - +
62A SER 3.2 1.3 - - - -
63A LYS* 3.4 34.0 + - - +
64A ASP* 3.2 31.7 + - - +
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Residues in contact with VAL 61 (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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22A TRP* 4.0 31.0 - - + +
57A VAL* 3.2 22.0 - - + +
58A TRP* 3.5 34.1 - - + +
59A GLU 3.3 0.6 - - - -
60A GLU* 1.3 77.3 - - - +
62A SER* 1.3 58.0 + - - +
64A ASP* 3.2 21.8 - - - +
79A VAL* 3.8 19.9 - - + +
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Residues in contact with SER 62 (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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58A TRP 3.6 1.6 + - - -
59A GLU* 2.5 24.4 + - - -
61A VAL* 1.3 80.2 - - - +
63A LYS* 1.3 68.2 + - - +
64A ASP 3.6 3.8 + - - +
65A PRO* 5.0 1.0 - - - +
79A VAL* 3.6 11.0 - - - +
80A SER* 3.4 46.3 - - - -
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Residues in contact with LYS 63 (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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59A GLU* 3.2 36.4 + - - +
60A GLU* 3.4 34.3 + - - +
61A VAL 3.4 0.2 - - - -
62A SER* 1.3 83.9 + - - +
64A ASP* 1.3 58.7 + - - +
65A PRO* 3.3 14.1 - - - +
80A SER 5.3 4.2 + - - -
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Residues in contact with ASP 64 (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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60A GLU* 3.2 20.3 + - - +
61A VAL* 3.2 17.6 - - - +
62A SER 4.4 2.3 - - - +
63A LYS* 1.3 77.3 - - - +
65A PRO* 1.3 69.4 - - - +
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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