Contacts of the helix formed by residues 61 - 80 (chain A) in PDB entry 3H1S
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 ASN 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A SER* 1.3 73.7 - - - +
62A GLY* 1.3 71.7 + - - +
64A ILE* 3.4 8.7 + - - +
65A PHE* 3.2 16.3 + - - -
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Residues in contact with GLY 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 1.3 78.8 - - - +
63A GLY* 1.3 59.2 + - - -
65A PHE* 3.2 5.6 + - - +
66A ASN* 3.0 35.9 + - - +
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.4 16.4 - - - +
61A ASN 3.6 0.2 + - - -
62A GLY* 1.3 68.4 - - - -
64A ILE* 1.3 63.9 + - - +
66A ASN* 4.4 8.3 - - - -
67A ASN* 2.9 31.9 + - - +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.8 11.5 - - + +
42A LEU* 3.7 43.0 - - + +
43A VAL* 4.2 5.6 - - + +
46A THR* 4.3 11.4 - - + +
48A HIS* 3.6 23.6 - - + +
56A ILE* 3.4 30.3 - - + -
60A SER* 3.6 8.1 - - - -
61A ASN 3.4 7.4 + - - +
62A GLY 3.3 1.0 - - - -
63A GLY* 1.3 76.0 - - - +
65A PHE* 1.3 59.5 + - - +
68A ALA* 2.8 28.6 + - - +
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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
----------------------------------------------------------
57A VAL* 3.4 30.1 - - + -
60A SER* 3.2 35.3 + - - +
61A ASN* 3.2 10.3 + - - -
62A GLY 3.2 9.5 + - - +
64A ILE* 1.3 79.1 - - - +
66A ASN* 1.3 72.9 + - - +
67A ASN 3.2 0.2 + - - -
68A ALA* 3.2 1.6 + - - -
69A ALA* 2.7 55.1 + - + +
141A ALA* 3.9 21.5 - - + -
142A GLY* 4.4 10.5 - - - -
143A CYS 4.4 1.8 - - - -
146A THR* 3.5 21.8 - - + -
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Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 5.2 0.2 - - - -
62A GLY* 3.0 23.1 + - - +
63A GLY* 3.9 8.7 - - - +
64A ILE 3.3 0.2 - - - -
65A PHE* 1.3 90.9 - - - +
67A ASN* 1.3 60.6 + - - +
70A GLN* 3.0 36.7 + - - +
141A ALA* 3.6 9.7 + - - +
118B PHE* 3.5 51.2 - - + +
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 3.5 38.7 - - - +
38A ASN* 3.2 36.1 + - - +
39A LEU* 4.0 14.4 - - + +
42A LEU* 3.6 11.4 - - + +
63A GLY* 2.9 23.5 + - - +
64A ILE 4.1 1.1 - - - +
66A ASN* 1.3 75.6 - - - +
68A ALA* 1.3 59.7 + - - +
70A GLN 3.5 0.5 + - - -
71A VAL* 3.0 34.8 + - - +
118B PHE* 6.0 1.2 - - - -
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Residues in contact with ALA 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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39A LEU* 3.7 18.9 - - + +
53A LEU* 3.7 11.6 - - + +
56A ILE* 3.7 26.0 - - + -
57A VAL* 3.8 13.9 - - + +
64A ILE 2.8 19.5 + - - +
65A PHE* 3.9 2.7 - - - +
67A ASN* 1.3 74.9 - - - +
69A ALA* 1.3 60.2 + - - +
71A VAL* 3.1 4.7 + - - +
72A PHE* 2.9 27.7 + - - +
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Residues in contact with ALA 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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57A VAL* 3.8 11.3 - - + +
65A PHE* 2.7 41.9 + - + +
68A ALA* 1.3 73.2 - - - +
70A GLN* 1.3 57.6 + - - +
72A PHE* 3.2 2.3 + - - +
73A ASN* 2.8 37.0 + - - +
141A ALA* 3.1 25.6 - - + +
143A CYS* 4.3 9.2 - - + -
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Residues in contact with GLN 70 (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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35A TYR* 3.1 54.0 + - + -
66A ASN 3.0 26.0 + - - +
67A ASN 3.9 0.4 - - - +
68A ALA 3.3 0.2 - - - -
69A ALA* 1.3 73.1 - - - +
71A VAL* 1.3 65.6 + - - +
73A ASN* 3.4 8.1 + - - -
74A HIS* 2.7 46.7 + - - +
122A TRP* 3.1 24.3 + - - -
140A ASN 3.5 9.3 - - - +
141A ALA* 3.5 9.3 - - + -
158A TRP* 3.3 26.0 - - - +
118B PHE* 4.0 3.6 - - + -
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Residues in contact with VAL 71 (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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3A PHE* 6.0 4.5 - - + -
4A GLU 5.6 2.7 - - - +
6A PRO* 5.7 2.5 - - + -
32A HIS* 3.2 23.3 - - + +
35A TYR* 3.6 8.1 - - + +
36A VAL* 3.6 44.0 - - + +
39A LEU* 4.4 7.4 - - + -
53A LEU* 3.7 24.2 - - + -
67A ASN 3.0 20.9 + - - +
68A ALA 3.1 6.5 + - - +
70A GLN* 1.3 75.4 - - - +
72A PHE* 1.3 64.6 + - - +
75A THR* 3.2 26.3 + - - +
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 3.8 18.6 - - + +
54A GLU* 3.7 38.8 - - + -
57A VAL* 4.3 8.7 - - + -
68A ALA 2.9 13.8 + - - +
69A ALA 3.6 5.8 - - - +
71A VAL* 1.3 78.9 - - - +
73A ASN* 1.3 75.1 + - - +
75A THR* 3.5 4.2 + - - -
76A PHE* 3.0 48.5 + + + +
124A TRP* 4.6 3.8 - + - -
143A CYS* 3.8 18.2 - - - -
145A LEU* 3.9 19.5 - - + -
151A PRO* 4.3 13.2 - - + -
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Residues in contact with ASN 73 (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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69A ALA 2.8 23.5 + - - +
70A GLN* 3.4 14.3 + - - +
72A PHE* 1.3 76.4 - - - +
74A HIS* 1.3 56.3 + - - +
76A PHE* 3.4 5.5 + - - +
77A TYR* 2.9 28.9 + - - +
122A TRP* 3.5 32.8 - - + +
124A TRP* 3.4 22.9 - - + -
141A ALA 3.2 25.5 + - - -
142A GLY 3.4 10.9 + - - -
143A CYS* 3.4 18.5 - - - -
154A THR* 4.3 1.0 - - - +
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Residues in contact with HIS 74 (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 HIS* 3.2 21.9 + + - -
31A HIS* 5.1 0.2 - - - +
32A HIS* 3.5 29.2 - + + +
35A TYR* 3.3 33.3 - + - -
70A GLN* 2.7 44.1 + - - +
73A ASN* 1.3 74.3 - - - +
75A THR* 1.3 64.9 + - - +
77A TYR* 3.2 5.8 + + - +
78A TRP* 2.9 37.5 + + - +
122A TRP* 3.8 10.9 - + - -
156A ASP* 3.4 4.2 + - - -
160A HIS* 3.7 1.4 + - - -
1001A FE 2.1 31.6 - - - -
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Residues in contact with THR 75 (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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6A PRO* 3.4 28.6 - - + +
32A HIS* 3.2 19.4 + - - -
53A LEU* 5.7 1.7 - - - +
71A VAL* 3.2 17.8 + - - +
72A PHE* 3.9 5.2 - - - -
74A HIS* 1.3 75.6 - - - +
76A PHE* 1.3 62.7 + - - +
78A TRP* 3.4 7.8 + - - +
79A ASN* 3.0 40.7 + - - +
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Residues in contact with PHE 76 (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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72A PHE* 3.0 39.7 + + + +
73A ASN* 3.5 6.7 - - - +
75A THR* 1.3 75.8 - - - +
77A TYR* 1.3 62.6 + - - +
79A ASN* 3.2 10.8 + - - +
80A CYS* 3.1 45.7 + - - -
124A TRP* 4.0 7.6 - + + -
151A PRO* 3.3 41.7 - - + -
152A LEU 3.5 21.5 - - - -
153A LEU* 3.7 7.4 - - - -
154A THR* 3.9 11.9 - - + -
185A PHE* 3.7 22.2 - + - -
189A GLN* 4.1 10.3 - - + -
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Residues in contact with TYR 77 (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 ILE* 3.7 18.0 - - - +
27A HIS* 3.8 17.2 + + - -
73A ASN 2.9 17.4 + - - +
74A HIS* 3.5 7.0 - + - +
76A PHE* 1.3 76.9 - - - +
78A TRP* 1.3 101.6 + + - +
80A CYS* 2.9 20.5 + - - +
81A LEU* 3.4 29.5 + - + +
122A TRP* 3.9 7.0 - + + -
154A THR* 3.6 25.3 - - + +
155A PHE* 4.2 4.7 - + - -
156A ASP* 3.5 34.5 - - + -
161A ALA* 4.4 5.5 + - - +
173A TYR* 2.7 24.3 + - - -
177A LEU* 4.5 3.5 - - + +
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Residues in contact with TRP 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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6A PRO* 6.4 0.2 - - + -
8A LEU* 3.8 12.1 - - + -
9A PRO* 4.0 16.1 - - + +
10A TYR* 2.7 38.9 + - - +
19A ILE* 5.3 2.5 - - + -
23A THR* 6.0 0.2 - - + -
24A ILE* 3.8 24.2 - - + -
27A HIS* 3.6 38.6 - + + -
28A TYR* 3.5 40.1 - + + -
32A HIS* 3.0 30.1 - + - -
74A HIS* 2.9 29.7 + + + +
75A THR* 3.4 6.7 + - - +
76A PHE 3.4 0.2 - - - -
77A TYR* 1.3 100.0 - + - +
79A ASN* 1.3 61.2 + - - +
81A LEU* 3.2 18.4 + - + +
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Residues in contact with ASN 79 (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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9A PRO* 3.6 20.4 - - - +
75A THR* 3.0 33.1 + - - +
76A PHE* 3.2 4.5 + - - +
77A TYR 3.2 0.6 - - - -
78A TRP* 1.3 76.2 - - - +
80A CYS* 1.3 58.5 + - - +
81A LEU 3.2 3.0 + - - +
182A ASN* 3.4 22.5 + - - -
185A PHE* 3.4 44.9 - - + +
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Residues in contact with CYS 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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76A PHE* 3.1 48.3 + - - -
77A TYR 2.9 10.8 + - - +
79A ASN* 1.3 74.7 - - - +
81A LEU* 1.3 64.5 + - + +
152A LEU 4.2 0.2 - - - -
153A LEU* 3.7 22.0 - - + +
154A THR 3.6 22.9 - - - +
181A VAL* 3.4 9.5 - - - +
182A ASN* 2.8 25.2 + - - -
185A PHE* 3.8 12.6 - - - -
186A VAL* 5.3 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