Contacts of the helix formed by residues 50 - 71 (chain A) in PDB entry 1HV2
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A SER* 3.9 1.1 - - - -
11A LYS* 3.9 28.4 + - + +
48A GLN 3.7 2.6 + - - +
49A PHE* 1.3 72.3 - - - +
51A SER* 1.3 69.0 + - - +
52A HIS* 2.7 48.7 + - + +
53A ILE* 2.9 17.7 + - + +
54A LEU* 2.9 12.0 + - - +
89A GLU* 2.8 18.7 + - - +
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A SER* 2.8 27.4 + - - -
11A LYS* 4.8 1.8 - - - +
14A LYS* 3.1 28.7 - - - +
16A TYR* 3.3 21.1 + - - -
50A ASP* 1.3 75.8 + - - +
52A HIS* 1.3 57.4 + - - +
54A LEU* 4.4 0.4 - - - -
55A GLU* 2.8 33.6 + - - +
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Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 4.9 0.7 - - - -
50A ASP* 2.7 35.7 + - + +
51A SER* 1.3 73.8 - - - +
53A ILE* 1.3 86.4 + - + +
55A GLU* 3.6 11.6 - - - +
56A LYS* 3.5 9.5 + - - +
85A GLU* 4.1 21.1 + - + +
86A MET* 3.3 32.5 - - + +
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Residues in contact with ILE 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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49A PHE* 5.6 0.4 - - + -
50A ASP* 2.9 10.8 + - + +
52A HIS* 1.3 108.7 - - + +
54A LEU* 1.3 67.6 + - - +
56A LYS* 2.9 15.8 + - - +
57A ALA* 3.0 10.2 + - - +
85A GLU* 4.5 4.0 - - + +
86A MET* 3.8 33.9 - - + +
89A GLU* 3.4 34.5 - - + +
90A LEU* 3.4 34.8 - - + +
93A ALA* 4.4 8.3 - - + -
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Residues in contact with LEU 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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8A LEU* 3.6 25.6 - - + +
9A VAL 3.5 34.1 - - - +
10A SER* 3.6 16.4 - - - +
16A TYR* 4.1 6.5 - - + -
46A LEU* 4.3 23.8 - - + -
49A PHE* 5.3 5.8 - - + +
50A ASP 2.9 14.4 + - - +
51A SER* 3.9 3.1 - - - +
53A ILE* 1.3 75.7 - - - +
55A GLU* 1.3 53.9 + - - +
57A ALA* 3.0 12.6 + - + +
58A VAL* 2.8 51.9 + - + +
93A ALA* 4.7 7.6 - - + +
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Residues in contact with GLU 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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16A TYR* 2.8 40.0 + - + +
51A SER 2.8 20.6 + - - +
52A HIS* 3.6 12.4 - - - +
54A LEU* 1.3 71.8 - - - +
56A LYS* 1.3 62.7 + - - +
58A VAL* 3.4 10.0 - - + +
59A GLU* 2.8 34.3 + - + +
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Residues in contact with LYS 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 HIS 3.5 1.8 + - - +
53A ILE 2.9 9.3 + - - +
55A GLU* 1.3 81.6 + - - +
57A ALA* 1.3 60.8 + - - +
59A GLU* 3.1 16.1 + - - +
60A TYR* 2.8 26.7 + - - +
80A PHE* 3.6 32.8 - - + -
81A GLU 3.8 21.8 - - - +
82A ILE* 4.9 2.0 - - + -
83A PRO* 5.4 0.7 - - + -
86A MET* 3.6 32.7 - - + +
90A LEU* 3.5 20.9 - - + -
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Residues in contact with ALA 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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53A ILE 3.0 7.8 + - - +
54A LEU* 3.0 14.7 + - + +
56A LYS* 1.3 78.0 - - - +
58A VAL* 1.3 61.0 + - + +
60A TYR* 3.4 12.6 - - - +
61A LEU 3.6 0.5 + - - -
90A LEU* 4.3 7.0 - - + +
93A ALA* 3.8 31.0 - - + -
94A ALA 4.5 7.0 - - - +
97A LEU* 3.3 23.6 - - + +
158B LEU* 4.2 14.4 - - + -
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Residues in contact with VAL 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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8A LEU* 3.4 38.1 - - + -
16A TYR* 4.2 13.9 - - + -
18A ILE* 3.9 25.4 - - + +
54A LEU* 2.8 34.0 + - + +
55A GLU* 3.4 17.7 - - + +
57A ALA* 1.3 69.7 - - + +
59A GLU* 1.3 63.1 + - - +
60A TYR 3.2 0.2 - - - -
61A LEU* 2.8 25.6 + - - +
62A ASN* 3.0 12.2 + - - +
97A LEU* 4.9 2.5 - - + -
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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 GLU* 2.8 26.8 + - + +
56A LYS* 3.5 25.8 - - - +
58A VAL* 1.3 74.0 - - - +
60A TYR* 1.3 55.7 + - - +
62A ASN* 2.8 33.8 + - - +
63A TYR* 2.8 35.0 + - + +
80A PHE* 4.1 6.5 - - + -
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Residues in contact with TYR 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 LYS 2.8 8.3 + - - +
57A ALA 3.4 11.9 - - - +
58A VAL 3.2 0.2 - - - -
59A GLU* 1.3 75.8 - - - +
61A LEU* 1.3 61.3 + - + +
63A TYR* 3.4 18.9 - + - +
64A ASN* 2.7 57.4 + - + +
80A PHE* 3.6 33.3 - + + -
97A LEU* 4.8 6.1 - - + -
99A ILE* 3.9 15.5 - - + -
157B THR* 2.7 42.7 + - - +
158B LEU* 3.9 38.6 - - + -
161B ARG* 6.2 2.0 - - + -
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Residues in contact with LEU 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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8A LEU* 5.6 2.2 - - + -
18A ILE* 3.9 15.0 - - + -
22A ALA* 3.2 32.9 - - + +
23A ALA* 3.8 13.0 - - - +
25A ILE* 3.8 28.4 - - + +
26A SER* 4.0 10.3 - - - +
29A LEU* 6.0 0.9 - - + -
57A ALA 3.6 3.0 + - - +
58A VAL* 2.8 22.9 + - + +
60A TYR* 1.3 76.2 - - + +
62A ASN* 1.3 56.5 + - - +
64A ASN* 3.1 5.7 + - - +
65A LEU* 2.9 27.2 + - - +
97A LEU* 4.3 32.1 - - + -
99A ILE* 5.0 9.0 - - + -
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Residues in contact with ASN 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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22A ALA* 4.5 8.6 - - + +
58A VAL 3.0 11.5 + - - +
59A GLU* 2.8 35.3 + - - +
61A LEU* 1.3 74.8 - - - +
63A TYR* 1.3 56.2 + - - +
65A LEU* 2.9 17.1 + - - +
66A LYS* 2.8 46.6 + - - +
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Residues in contact with TYR 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* 2.8 22.9 + - + +
60A TYR* 3.4 22.2 - + - +
62A ASN* 1.3 75.7 - - - +
64A ASN* 1.3 59.8 + - - +
66A LYS* 3.3 7.8 + - - +
67A TYR* 2.8 39.7 + + + +
77A ILE* 3.4 27.4 - - + +
78A PRO* 2.7 44.5 + - + -
79A GLU* 4.5 0.5 - - - -
80A PHE* 3.6 43.2 + + + +
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Residues in contact with ASN 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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25A ILE* 4.0 16.4 - - + +
60A TYR* 2.7 46.1 + - + +
61A LEU* 3.1 10.7 + - - +
63A TYR* 1.3 76.7 - - - +
65A LEU* 1.3 53.7 + - - +
67A TYR* 3.4 11.2 + - - +
68A SER* 2.7 49.7 + - - -
99A ILE* 3.0 21.7 - - - +
157B THR* 5.3 0.7 - - - +
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Residues in contact with LEU 65 (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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19A SER* 5.3 2.5 - - - -
21A SER* 3.6 44.0 - - - +
22A ALA* 3.8 14.8 - - + +
25A ILE* 3.6 14.9 - - + +
61A LEU 2.9 12.4 + - - +
62A ASN* 2.9 16.6 + - - +
64A ASN* 1.3 74.9 - - - +
66A LYS* 1.3 63.6 + - + +
68A SER* 3.1 8.9 + - - -
69A GLY* 2.8 28.0 + - - +
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Residues in contact with LYS 66 (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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62A ASN* 2.8 40.7 + - - +
63A TYR* 3.6 8.5 - - - +
65A LEU* 1.3 76.2 - - + +
67A TYR* 1.3 52.9 + - - +
69A GLY* 3.1 3.1 + - - +
70A VAL* 2.8 44.3 + - - +
77A ILE* 4.0 14.6 - - + -
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Residues in contact with TYR 67 (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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63A TYR* 2.8 30.3 + + + +
64A ASN* 3.5 14.1 - - - +
66A LYS* 1.3 71.4 - - - +
68A SER* 1.3 64.1 + - - +
70A VAL* 3.4 6.3 - - - +
71A SER* 2.8 30.0 + - - -
73A ASP* 2.7 58.6 + - - +
77A ILE* 3.9 21.8 - - + +
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Residues in contact with SER 68 (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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25A ILE* 4.9 3.2 - - - +
64A ASN* 2.7 37.0 + - - -
65A LEU* 3.4 10.9 - - - -
67A TYR* 1.3 78.7 - - - +
69A GLY* 1.3 56.8 + - - +
71A SER* 2.7 32.8 + - - +
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Residues in contact with GLY 69 (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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65A LEU* 2.8 18.7 + - - +
66A LYS* 3.6 3.1 - - - -
68A SER* 1.3 72.5 - - - +
70A VAL* 1.3 61.5 + - - +
71A SER* 3.5 5.2 + - - -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 2.8 31.0 + - + +
67A TYR* 3.4 5.8 - - - +
69A GLY* 1.3 73.0 - - - +
71A SER* 1.3 54.6 + - - +
72A GLU* 2.7 26.9 + - + +
73A ASP 4.0 7.2 - - - +
74A ASP* 3.9 14.4 - - - +
75A ASP* 3.7 47.3 - - + +
77A ILE* 4.1 13.7 - - + -
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 2.8 21.7 + - - +
68A SER* 2.7 20.9 + - - +
69A GLY 3.5 6.3 + - - -
70A VAL* 1.3 71.2 - - - +
72A GLU* 1.3 65.5 + - - +
73A ASP* 2.8 17.6 + - - -
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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