Contacts of the strand formed by residues 33 - 44 (chain A) in PDB entry 1HS6
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 THR 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A SER 3.6 0.9 - - - +
27A VAL 3.6 0.3 - - - -
28A ASP* 2.6 59.1 + - - +
31A ARG* 3.4 22.4 - - + +
32A ARG* 1.3 77.1 - - - +
34A LEU* 1.3 61.6 - - - +
35A THR* 3.8 14.2 + - - -
107A GLU* 4.4 15.2 - - + +
108A THR* 3.3 23.6 - - - +
110A PRO* 4.6 6.5 - - + -
117A TRP* 3.2 11.3 - - - -
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Residues in contact with LEU 34 (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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23A LEU* 5.8 2.5 - - + -
25A CYS* 3.9 19.7 - - + -
26A SER 3.1 18.8 - - - +
27A VAL* 3.3 29.4 - - + -
33A THR* 1.3 71.2 - - - +
35A THR* 1.3 63.1 + - - +
106A PHE* 3.9 9.7 - - + +
107A GLU* 3.4 3.6 - - - +
108A THR* 3.0 46.2 + - + +
115A LEU* 5.1 8.7 - - + -
117A TRP* 5.0 3.8 - - + -
131A LEU* 5.0 8.3 - - + -
143A ILE* 4.1 24.5 - - + -
204A LEU* 4.0 20.2 - - + -
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Residues in contact with THR 35 (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 CYS* 3.1 6.5 - - - -
26A SER* 2.8 37.9 + - - -
28A ASP* 5.6 1.4 - - - +
33A THR* 3.8 11.8 + - - -
34A LEU* 1.3 80.6 + - - +
36A GLY* 1.3 64.5 + - - +
106A PHE* 3.4 11.2 - - - +
107A GLU* 3.6 25.9 - - + +
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Residues in contact with GLY 36 (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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24A ARG 3.4 8.7 - - - -
25A CYS* 4.1 2.2 - - - -
35A THR* 1.3 82.9 - - - +
37A THR* 1.3 62.9 - - - +
105A SER* 3.4 5.0 + - - -
106A PHE* 2.8 49.7 + - - +
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Residues in contact with THR 37 (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 HIS* 3.6 3.6 + - - +
23A LEU* 3.0 18.4 - - - +
24A ARG* 2.9 43.8 + - - +
36A GLY* 1.3 77.6 - - - -
38A ALA* 1.3 62.3 + - - +
39A ALA* 3.8 1.2 + - - +
103A GLU* 3.8 30.8 + - + +
104A ILE 2.8 6.1 - - - +
105A SER* 3.6 22.4 - - - +
106A PHE* 3.6 4.4 - - - -
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Residues in contact with ALA 38 (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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21A LEU* 3.8 18.6 - - + -
22A HIS 3.8 2.9 - - - -
23A LEU* 4.5 1.6 - - + -
37A THR* 1.3 74.6 - - - +
39A ALA* 1.3 60.6 + - - +
40A LEU* 3.4 8.3 + - + +
102A ILE 3.1 6.4 - - - +
103A GLU* 4.3 0.4 - - - -
104A ILE* 2.6 41.3 + - + +
106A PHE* 3.6 19.0 - - + -
144A LEU* 4.4 12.8 - - + -
145A PRO* 4.5 4.7 - - + +
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Residues in contact with ALA 39 (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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20A HIS* 3.8 1.2 - - - +
21A LEU* 3.3 4.0 - - - +
22A HIS* 2.7 59.6 + - + +
37A THR* 3.8 1.9 - - - -
38A ALA* 1.3 70.6 - - - +
40A LEU* 1.3 62.2 + - - +
41A THR* 4.0 1.3 + - - -
101A VAL* 4.6 11.9 - - + -
102A ILE 3.4 6.7 - - - +
103A GLU* 4.0 20.8 - - + +
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Residues in contact with LEU 40 (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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18A THR* 4.4 15.5 - - + +
20A HIS 3.5 4.0 - - - +
21A LEU* 3.2 37.9 - - + -
38A ALA* 4.1 9.0 - - + +
39A ALA* 1.3 74.1 - - - +
41A THR* 1.3 61.7 + - - +
42A VAL* 3.5 15.4 + - + -
54A LEU* 3.7 31.4 - - + -
100A ILE 3.6 0.2 - - - +
101A VAL* 3.3 4.6 - - - -
102A ILE* 2.8 42.0 + - + +
104A ILE* 4.3 5.6 - - + -
144A LEU* 5.2 1.6 - - + -
145A PRO 3.7 23.3 - - - +
146A CYS* 4.6 5.4 - - + -
154A LEU* 5.8 0.7 - - + -
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Residues in contact with THR 41 (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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18A THR* 3.4 3.3 - - - +
19A LYS* 2.6 40.7 + - + -
20A HIS* 2.8 36.3 + - + +
39A ALA 4.0 1.1 + - - -
40A LEU* 1.3 72.1 - - - +
42A VAL* 1.3 57.9 + - - +
99A GLU* 3.8 28.5 - - + +
100A ILE 3.6 10.8 - - - +
101A VAL* 4.1 13.8 - - + +
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Residues in contact with VAL 42 (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 CYS* 3.7 33.9 - - + -
17A ARG 3.6 6.5 - - - +
18A THR* 3.9 18.6 - - - +
19A LYS* 4.9 0.4 - - - -
40A LEU* 4.2 20.0 - - + +
41A THR* 1.3 77.2 - - - +
43A GLN* 1.3 64.4 + - - +
44A SER 4.2 0.7 - - - +
49A LEU* 5.5 1.8 - - + -
52A LEU* 4.9 9.9 - - + -
54A LEU* 5.9 2.7 - - + -
94A LEU* 4.8 1.5 - - + +
98A GLN 3.9 0.2 - - - +
99A GLU* 3.0 26.4 - - - +
100A ILE* 2.9 31.8 + - + +
102A ILE* 4.3 12.6 - - + -
147A GLN* 5.3 0.2 - - - +
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Residues in contact with GLN 43 (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 CYS* 3.1 3.5 - - - -
17A ARG* 2.7 42.7 + - - +
19A LYS* 3.0 43.8 + - + +
42A VAL* 1.3 74.3 - - - +
44A SER* 1.3 70.2 + - - +
45A GLN* 2.9 27.8 + - - +
97A ASN* 3.9 33.3 + - - +
98A GLN 3.5 2.7 - - - +
99A GLU* 3.5 19.7 - - - +
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Residues in contact with SER 44 (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 VAL 3.8 4.7 - - - -
42A VAL 4.2 0.6 - - - -
43A GLN* 1.3 76.4 - - - +
45A GLN* 1.3 64.9 + - - +
46A GLU 2.5 28.3 + - - -
49A LEU* 3.5 21.7 - - - +
94A LEU* 3.7 19.3 - - - +
95A SER 3.5 17.3 - - - -
97A ASN* 2.9 23.9 + - - -
98A GLN 2.7 13.5 + - - -
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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