Contacts of the helix formed by residues 47 - 65 (chain A) in PDB entry 1HHS
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 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.6 18.3 - - + +
44A LEU* 3.0 23.8 + - + +
45A SER 3.4 0.6 - - - -
46A VAL* 1.3 76.8 - - - +
48A PRO* 1.3 73.0 - - - +
49A ARG* 2.8 68.2 + - - +
50A PHE* 3.0 14.9 + - + +
51A LEU* 3.0 10.9 + - - +
255B GLN 3.8 17.6 - - - +
256B TYR* 4.7 1.2 - - - -
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Residues in contact with PRO 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL 3.1 8.3 - - - +
47A ASP* 1.3 89.8 - - - +
49A ARG* 1.3 64.0 + - + +
51A LEU* 3.5 8.1 + - + +
52A SER* 3.0 24.1 + - - -
259A ASP* 5.6 12.1 - - + +
261A PRO* 6.4 0.4 - - + -
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Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLY 5.6 0.2 + - - -
43A LEU* 4.7 3.6 - - - +
47A ASP* 2.8 53.2 + - - +
48A PRO* 1.3 75.6 - - + +
50A PHE* 1.3 57.7 + - - +
52A SER* 3.2 5.7 + - - -
53A PHE 2.9 24.3 + - - -
578A ALA* 3.4 34.8 + - - +
579A PHE* 3.5 40.0 + - + +
256B TYR* 4.0 23.9 - - - -
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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
----------------------------------------------------------
39A THR* 4.0 25.8 - - + -
40A TYR* 5.8 1.1 - + - -
43A LEU* 4.0 19.7 - - + -
44A LEU 4.1 1.3 - - - -
45A SER* 3.5 26.5 - - - -
47A ASP* 3.0 21.7 + - + +
49A ARG* 1.3 78.7 - - - +
51A LEU* 1.3 57.6 + - - +
53A PHE* 3.2 13.0 + + - +
54A LYS* 2.9 48.4 + - + +
91A ASN* 5.0 0.2 - - - -
526A PHE* 3.3 50.5 - + + -
575A TRP* 4.0 18.4 - + - -
579A PHE* 3.7 10.0 - + + -
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER 3.3 23.8 - - - +
46A VAL* 3.6 18.6 - - - +
47A ASP 3.0 16.0 + - - +
48A PRO* 4.0 7.0 - - + +
50A PHE* 1.3 73.7 - - - +
52A SER* 1.3 61.8 + - - +
54A LYS* 3.3 8.4 + - + +
55A ASN* 2.8 26.0 + - - +
89A HIS 4.8 3.4 - - - +
90A MET* 3.8 23.1 - - + -
259A ASP 4.1 4.7 - - - +
261A PRO* 3.6 38.8 - - + -
264A PHE* 3.4 35.7 - - + -
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Residues in contact with SER 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO 3.0 18.6 + - - -
49A ARG* 3.5 7.2 - - - -
51A LEU* 1.3 76.2 - - - +
53A PHE* 1.3 58.7 + - - +
55A ASN* 3.2 8.2 + - - +
56A GLU* 2.9 31.6 + - - +
261A PRO* 5.6 1.1 - - - +
578A ALA* 4.9 7.2 - - - +
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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
----------------------------------------------------------
49A ARG 2.9 13.0 + - - +
50A PHE* 3.3 22.9 - + - +
52A SER* 1.3 77.0 - - - +
54A LYS* 1.3 64.7 + - + +
56A GLU* 3.3 4.8 + - - +
57A LEU* 2.9 58.4 + - + +
526A PHE* 3.7 45.3 - + - -
571A ILE* 3.7 25.1 - - + -
574A CYS* 3.6 16.6 - - + +
575A TRP* 3.6 39.7 - + + -
578A ALA* 3.7 14.3 - - + +
579A PHE* 4.3 2.2 - - + -
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Residues in contact with LYS 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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45A SER 5.3 1.2 + - - -
50A PHE* 2.9 36.9 + - + +
51A LEU* 3.7 8.5 - - + +
53A PHE* 1.3 90.2 - - + +
55A ASN* 1.3 61.1 + - - +
57A LEU* 4.6 0.2 - - - -
58A SER* 2.8 31.6 + - - -
87A MET* 3.0 48.7 + - + +
89A HIS 3.8 5.9 + - - -
91A ASN* 3.1 30.3 - - - +
264A PHE* 3.9 17.7 - - + -
526A PHE* 3.2 24.1 + - + -
527A SER* 3.2 10.1 + - - -
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Residues in contact with ASN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU 2.8 20.9 + - - +
52A SER* 3.2 8.4 + - - +
54A LYS* 1.3 76.6 - - - +
56A GLU* 1.3 67.8 + - - +
58A SER* 3.2 10.0 + - - -
59A ARG* 2.8 47.0 + - - +
88A ARG* 2.9 27.9 + - - +
261A PRO* 5.8 4.0 - - + -
264A PHE* 3.8 12.7 - - + -
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER* 2.9 16.5 + - - +
53A PHE* 3.9 3.7 - - - +
55A ASN* 1.3 84.3 - - - +
57A LEU* 1.3 62.9 + - - +
59A ARG* 3.9 4.8 - - - +
60A TYR* 3.0 23.0 + - + +
573A ARG* 2.9 24.6 + - - +
574A CYS* 3.5 21.6 - - + +
577A ASN* 2.9 34.9 + - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 2.9 48.8 + - + +
54A LYS 4.3 1.6 - - - +
56A GLU* 1.3 73.4 - - - +
58A SER* 1.3 63.0 + - - +
60A TYR* 3.2 2.3 + - + +
61A LEU* 2.9 47.7 + - + +
87A MET* 4.1 20.2 - - + -
522A LEU* 4.2 11.4 - - + -
526A PHE* 4.4 1.1 - - + -
570A ALA* 3.8 34.5 - - + +
571A ILE* 4.1 15.7 - - + +
574A CYS* 3.8 13.9 - - + -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS 2.8 23.0 + - - -
57A LEU* 1.3 76.9 - - - +
59A ARG* 1.3 59.3 + - - +
62A THR* 2.9 32.2 + - - -
84A PHE* 3.4 29.2 - - - +
85A PHE* 3.6 11.5 - - - -
87A MET* 3.8 15.6 - - - -
88A ARG* 2.9 28.5 + - - -
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Residues in contact with ARG 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 ASN* 2.8 43.9 + - - +
56A GLU* 3.9 3.8 - - - +
58A SER* 1.3 81.5 + - - +
60A TYR* 1.3 58.7 + - - +
62A THR* 3.8 1.4 - - - -
63A ASP* 2.9 34.4 + - - +
85A PHE* 3.9 15.7 - - + -
88A ARG* 4.0 8.4 - - - +
213A LEU* 4.5 13.8 - - + +
218A GLY 5.4 3.2 + - - -
220A PHE* 3.3 31.5 - - - -
262A ASP* 4.0 11.7 + - - +
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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 GLU* 3.0 19.6 + - + +
57A LEU* 3.7 4.9 - - - +
59A ARG* 1.3 74.9 - - - +
61A LEU* 1.3 72.5 + - + +
63A ASP* 3.3 2.7 + - - -
64A HIS* 2.9 74.4 + + + +
65A PHE* 4.6 6.1 - + - -
566A ASP 5.6 0.7 - - - -
570A ALA* 3.8 25.6 - - + -
573A ARG* 3.1 38.2 + - - +
574A CYS* 5.0 0.2 - - - -
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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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57A LEU* 2.9 38.1 + - + +
60A TYR* 1.3 78.2 - - + +
62A THR* 1.3 58.6 + - - +
65A PHE* 2.7 57.7 + - + +
84A PHE* 3.5 28.4 - - + -
87A MET* 5.3 0.7 - - + -
522A LEU* 3.7 29.6 - - + -
567A VAL* 4.3 21.8 - - + -
570A ALA* 3.8 25.1 - - + -
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Residues in contact with THR 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 SER 2.9 22.4 + - - -
59A ARG 3.8 1.8 - - - -
61A LEU* 1.3 79.8 - - - +
63A ASP* 1.3 64.5 + - - +
65A PHE 3.6 5.2 + - - -
66A PRO* 3.7 15.7 - - + +
83A ASN* 3.6 22.8 - - + +
84A PHE* 2.9 29.9 + - - -
85A PHE* 3.5 24.9 - - + -
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Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 2.9 19.7 + - - +
60A TYR* 3.6 4.5 - - - +
62A THR* 1.3 81.1 - - - +
64A HIS* 1.3 73.1 + - + +
66A PRO* 4.0 7.6 - - - +
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Residues in contact with HIS 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 TYR* 2.9 67.7 + + + +
63A ASP* 1.3 87.2 - - + +
65A PHE* 1.3 89.2 + - + +
66A PRO* 3.4 7.7 - - - +
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 4.6 8.5 - + - -
61A LEU* 2.7 48.8 + - + +
62A THR* 3.8 2.1 - - - +
63A ASP 3.5 0.2 - - - -
64A HIS* 1.3 97.6 - - + +
66A PRO* 1.3 68.6 - - - +
67A ALA 3.7 0.2 + - - -
78A ASN* 4.0 11.2 - - + +
80A VAL* 3.4 17.1 - - + +
82A THR 4.9 0.5 - - - +
83A ASN* 5.9 0.5 - - - -
84A PHE* 3.6 9.9 - - + -
563A ILE* 3.7 47.1 - - + -
566A ASP* 3.5 35.2 - - + -
567A VAL* 5.5 0.2 - - + -
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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
------------------------------------------------------------
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