Contacts of the strand formed by residues 17 - 25 (chain A) in PDB entry 3SHD
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 LYS 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL 3.8 0.2 - - - +
13A HIS* 3.3 7.2 + - - -
14A ALA 2.9 31.7 + - - +
15A GLU* 3.2 15.7 - - + +
16A GLY* 1.3 86.6 - - - +
18A PHE* 1.3 67.5 + - - +
91A ILE* 4.3 14.1 - - + -
106A TRP* 4.1 20.5 + - + +
107A VAL 3.4 16.6 - - - +
108A SER* 3.9 26.6 - - - +
111A GLU* 4.9 3.6 + - - -
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Residues in contact with PHE 18 (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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11A VAL* 3.6 24.7 - - + -
12A VAL 3.3 9.9 - - - +
13A HIS* 3.4 29.4 - + + -
16A GLY 4.8 2.5 - - - -
17A LYS* 1.3 78.7 - - - +
19A LEU* 1.3 64.5 + - - +
20A VAL* 3.8 0.7 + - - +
33A GLN* 6.0 1.1 - - - +
105A ARG 3.7 0.5 - - - +
106A TRP* 3.3 4.4 - - - -
107A VAL* 2.6 47.7 + - - +
109A ALA* 3.6 35.2 - - + -
112A ILE* 3.8 15.4 - - + +
127A ILE* 4.1 16.4 - - + -
130A TYR* 3.4 37.7 - + - -
131A GLN* 4.6 7.6 - - + -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A CYS 5.1 0.5 - - - +
12A VAL* 3.0 28.4 + - + +
18A PHE* 1.3 71.6 - - - +
20A VAL* 1.3 68.8 + - - +
32A ASN 4.4 0.3 - - - +
33A GLN* 4.5 5.4 + - - +
34A PRO* 3.7 26.3 - - + +
52A LEU* 4.4 4.3 - - + -
56A THR* 3.5 30.5 - - + -
58A ILE* 4.3 13.9 - - + -
94A THR* 4.2 2.9 - - + -
104A CYS* 3.7 22.7 - - + -
105A ARG 3.5 13.0 - - - +
106A TRP* 3.6 44.3 - - + +
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Residues in contact with VAL 20 (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 PHE 4.5 2.2 - - - +
19A LEU* 1.3 83.2 - - - +
21A VAL* 1.3 63.3 + - - +
31A TRP* 3.6 45.5 - - + -
32A ASN 3.4 14.6 - - - +
33A GLN* 5.0 4.5 - - - +
104A CYS* 3.3 6.9 - - - +
105A ARG* 2.8 49.5 + - + +
107A VAL* 5.0 2.7 - - + -
112A ILE* 3.9 33.2 - - + -
123A VAL* 5.1 5.2 - - + -
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Residues in contact with VAL 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 VAL* 1.3 78.6 - - - +
22A GLU* 1.3 59.0 + - - +
23A GLU* 3.8 17.0 + - - +
30A LEU 3.3 5.4 - - - +
31A TRP* 3.4 1.9 - - - -
32A ASN* 2.8 45.7 + - - +
33A GLN 3.6 8.1 - - - +
34A PRO* 4.2 5.8 - - + -
55A GLU* 3.5 50.0 - - + +
56A THR* 4.0 16.8 - - + -
101A ILE* 3.9 12.3 - - + -
103A CYS 3.6 2.2 - - - -
104A CYS* 4.1 5.2 - - - -
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Residues in contact with GLU 22 (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 VAL* 4.2 1.0 + - - +
21A VAL* 1.3 69.4 - - - +
23A GLU* 1.3 58.1 + - - +
29A ALA* 3.8 28.0 - - + +
30A LEU 3.3 7.0 - - - +
31A TRP* 3.0 29.4 + - + -
101A ILE* 3.5 3.3 - - - -
102A ASP* 2.7 43.3 + - + +
103A CYS* 2.9 34.1 + - - +
105A ARG* 3.2 29.7 + - + -
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Residues in contact with GLU 23 (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 VAL* 3.8 15.3 + - - +
22A GLU* 1.3 72.1 - - - +
24A THR* 1.3 62.4 + - - +
25A ILE* 3.2 17.1 + - + +
29A ALA* 4.3 1.1 - - - -
30A LEU 2.8 32.8 + - - +
32A ASN* 3.9 6.2 - - - +
100A ASP* 3.2 28.9 - - + +
101A ILE* 3.5 19.0 - - + +
102A ASP* 3.6 0.9 - - - -
119A ARG* 2.8 31.4 + - - +
157A SO4 2.7 32.7 + - - -
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Residues in contact with THR 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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23A GLU* 1.3 70.7 - - - +
25A ILE* 1.3 61.9 + - - +
26A ASN 4.1 1.0 + - - -
27A GLY* 3.8 28.3 - - - +
28A LYS 3.2 13.2 - - - +
29A ALA* 4.1 7.6 - - - +
100A ASP 4.4 3.3 + - - +
102A ASP* 2.5 30.2 + - - -
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Residues in contact with ILE 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 GLU* 3.4 22.7 - - + +
24A THR* 1.3 75.2 - - - +
26A ASN* 1.3 90.2 + - - +
27A GLY 3.5 0.2 - - - -
28A LYS* 2.6 22.8 + - - +
30A LEU* 3.5 29.0 - - + +
119A ARG* 3.8 29.6 - - - +
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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