Contacts of the strand formed by residues 16 - 28 (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 CYS 16 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A SER* 4.0 15.9 - - - -
12A PRO 3.1 14.0 + - - +
13A ALA* 3.4 2.1 - - - -
15A VAL* 1.3 83.8 - - - +
17A ARG* 1.3 70.6 + - - +
42A VAL* 3.7 20.4 - - + -
43A GLN 3.1 14.1 - - - +
45A GLN* 3.6 2.4 - - - +
49A LEU* 3.8 13.0 - - + -
52A LEU* 3.9 29.2 - - - -
53A VAL 5.8 0.2 - - - -
147A GLN* 3.2 20.8 + - - -
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Residues in contact with ARG 17 (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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13A ALA* 2.2 49.3 + - + +
14A SER* 4.1 4.4 - - - +
16A CYS* 1.3 81.7 - - - +
18A THR* 1.3 65.3 + - - +
19A LYS* 3.3 30.1 - - + +
42A VAL* 4.4 2.7 - - - -
43A GLN* 2.7 35.6 + - - +
45A GLN* 2.6 50.4 - - - +
147A GLN* 3.6 3.6 - - - -
152A VAL* 4.7 8.1 - - + -
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Residues in contact with THR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 1.3 73.1 - - - +
19A LYS* 1.3 63.0 + - - +
20A HIS 3.6 22.2 - - - +
40A LEU* 4.4 22.7 - - + +
41A THR 3.4 8.5 - - - +
42A VAL* 3.9 12.6 - - - +
54A LEU* 5.2 0.5 - - - +
146A CYS* 5.8 0.2 - - - -
147A GLN* 2.8 34.7 + - - +
152A VAL* 3.7 15.2 - - - +
153A LYS 3.3 17.7 - - - +
154A LEU* 3.7 20.2 - - + +
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Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 3.3 35.6 - - + +
18A THR* 1.3 76.7 - - - +
20A HIS* 1.3 60.5 + - + +
41A THR* 2.6 24.7 + - + +
42A VAL 4.9 0.2 - - - -
43A GLN* 3.0 44.1 - - + +
99A GLU* 5.0 6.5 - - - +
153A LYS 4.4 5.4 - - - -
154A LEU* 3.4 9.1 - - - +
155A THR* 3.0 25.3 + - - +
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Residues in contact with HIS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 3.6 8.8 - - - +
19A LYS* 1.3 83.9 - - + +
21A LEU* 1.3 80.1 + - - +
22A HIS* 3.9 7.7 - - + +
39A ALA 5.0 0.4 - - - -
40A LEU* 3.5 3.5 - - - -
41A THR* 2.8 45.2 + - - +
154A LEU* 3.7 1.1 - - - +
155A THR* 2.7 30.3 + - - +
156A TYR* 3.5 25.4 - - - -
157A THR* 3.1 27.5 + - + -
193A GLN 5.3 0.2 - - - -
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Residues in contact with LEU 21 (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* 1.3 82.0 + - - +
22A HIS* 1.3 74.2 + - - +
23A LEU* 4.1 16.8 - - + -
38A ALA* 3.8 21.8 - - + -
39A ALA 3.3 4.5 - - - +
40A LEU* 3.2 29.2 - - + -
144A LEU* 4.2 16.8 - - + -
154A LEU* 3.7 15.9 - - + -
155A THR 2.9 6.7 + - - -
156A TYR* 3.0 16.2 - - + +
157A THR 2.8 27.0 + - - +
202A ILE* 4.1 26.7 - - + -
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Residues in contact with HIS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 3.9 6.7 - - + +
21A LEU* 1.3 74.3 - - - +
23A LEU* 1.3 60.6 + - - +
24A ARG* 3.1 44.9 + - + +
37A THR* 3.6 3.1 + - - +
38A ALA* 3.7 0.7 - - - -
39A ALA* 2.7 55.0 + - + +
157A THR* 3.2 35.0 - - - +
159A GLU* 3.4 23.5 + - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.1 15.7 - - + -
22A HIS* 1.3 74.4 + - - +
24A ARG* 1.3 71.2 + - - +
25A CYS* 3.6 25.6 - - + -
34A LEU* 5.8 2.2 - - + -
37A THR 3.0 19.7 - - - +
38A ALA* 4.5 2.0 - - + -
106A PHE* 3.9 23.3 - - + -
143A ILE* 6.4 1.1 - - + -
144A LEU* 4.4 18.2 - - + -
156A TYR* 5.7 0.2 - - + -
157A THR 2.7 14.1 + - - +
158A ALA* 2.8 22.1 - - + +
159A GLU 2.6 33.5 + - - +
160A VAL* 5.8 0.2 - - + -
170A MET* 4.9 13.2 - - + -
204A LEU* 6.4 0.9 - - + -
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Residues in contact with ARG 24 (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* 3.1 31.8 + - + +
23A LEU* 1.3 73.9 - - - +
25A CYS* 1.3 62.5 + - - +
36A GLY* 3.4 1.0 - - - -
37A THR* 2.9 48.0 + - - +
103A GLU* 3.9 20.6 + - - -
159A GLU* 3.1 39.0 - - + +
188A ILE* 5.9 2.2 - - + -
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Residues in contact with CYS 25 (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* 3.6 30.1 - - + -
24A ARG* 1.3 76.3 - - - +
26A SER* 1.3 56.2 + - - +
34A LEU* 3.9 26.9 - - + -
35A THR 3.1 19.3 - - - +
36A GLY* 4.1 1.1 - - - -
106A PHE* 4.8 4.0 - - + -
159A GLU 3.0 6.5 + - - +
160A VAL* 3.1 24.6 - - - -
161A SER* 2.7 31.1 + - - -
188A ILE* 4.9 1.8 - - - +
204A LEU* 5.2 3.4 - - - -
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Residues in contact with SER 26 (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* 1.3 76.0 - - - +
27A VAL* 1.3 59.7 + - - +
28A ASP* 3.6 2.1 + - - +
33A THR 3.6 2.1 - - - +
34A LEU* 3.1 9.2 - - - +
35A THR* 2.8 35.8 + - - -
161A SER* 2.6 17.7 + - - -
186A ARG* 2.5 38.1 + - - -
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 1.3 72.7 + - - +
28A ASP* 1.3 55.7 + - - +
29A PHE* 3.6 18.0 + - + -
33A THR 3.6 2.0 - - - -
34A LEU* 3.3 18.4 - - + -
117A TRP* 3.5 30.1 - - + -
131A LEU* 3.7 13.9 - - + -
160A VAL* 3.8 24.9 - - + -
161A SER 2.9 9.7 + - - +
162A VAL* 4.0 10.5 - - + -
163A PRO* 3.9 4.2 - - - +
186A ARG* 2.3 31.1 + - - +
204A LEU* 4.4 5.2 - - + -
206A VAL* 4.0 11.0 - - + -
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Residues in contact with ASP 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 3.6 2.7 + - - +
27A VAL* 1.3 69.8 - - - +
29A PHE* 1.3 52.3 + - - +
30A THR* 2.8 33.8 + - - -
31A ARG* 2.9 36.3 + - - -
32A ARG* 2.6 30.1 + - - -
33A THR* 2.6 39.3 + - - +
35A THR* 5.6 1.6 - - - +
117A TRP* 4.0 2.0 - - - -
186A ARG* 5.1 4.9 - - - +
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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