Contacts of the strand formed by residues 17 - 23 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13I HIS* 3.2 11.6 + - - -
14I ALA 2.8 33.5 + - - +
15I GLU* 3.7 16.2 - - - +
16I GLY* 1.3 82.0 - - - +
18I PHE* 1.3 64.1 + - - +
19I LEU 4.3 0.2 - - - -
91I ILE* 4.6 9.9 - - + -
106I TRP* 3.5 46.8 + - + -
107I VAL* 3.5 11.4 - - - +
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Residues in contact with PHE 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I VAL* 3.9 17.9 - - + -
12I VAL 3.5 4.0 - - - +
13I HIS* 3.3 34.5 - + + -
16I GLY 5.1 3.6 - - - -
17I LYS* 1.3 74.4 - - - +
19I LEU* 1.3 65.5 + - - +
20I VAL* 3.2 4.9 + - - +
105I ARG 3.6 0.2 - - - +
106I TRP* 3.5 4.8 - - - -
107I VAL* 3.1 38.2 + - - +
108I SER 4.4 0.2 - - - -
109I ALA* 3.8 17.3 - - - -
112I ILE* 5.0 6.7 - - + -
127I ILE* 3.9 30.3 - - + -
130I TYR* 3.8 35.4 - + - -
131I GLN* 3.7 28.0 - - - -
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Residues in contact with LEU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I CYS 4.7 2.8 - - - +
11I VAL* 5.8 0.3 - - - -
12I VAL* 3.0 24.0 + - + +
18I PHE* 1.3 70.1 - - - +
20I VAL* 1.3 66.9 + - - +
21I VAL* 4.8 0.4 - - + -
33I GLN* 4.6 5.0 - - - +
34I PRO* 3.6 28.5 - - + +
52I LEU* 4.4 4.3 - - + -
56I THR* 3.8 20.4 - - + -
58I ILE* 3.8 28.3 - - + -
94I THR* 5.8 0.7 - - - -
104I CYS* 3.7 28.0 - - + -
105I ARG 3.8 6.5 - - - +
106I TRP* 3.5 39.6 - - + +
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Residues in contact with VAL 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I PHE 3.2 4.2 + - - +
19I LEU* 1.3 73.6 - - - +
21I VAL* 1.3 67.0 + - - +
31I TRP* 4.1 25.6 - - + +
32I ASN* 3.9 26.7 - - - +
33I GLN* 4.6 3.4 - - + +
104I CYS* 3.5 3.1 - - - +
105I ARG* 2.8 55.0 + - - +
107I VAL* 3.7 17.3 - - + -
112I ILE* 4.2 21.1 - - + -
123I VAL* 4.8 7.0 - - + -
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Residues in contact with VAL 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I LEU* 4.8 1.6 - - + -
20I VAL* 1.3 78.0 - - - +
22I GLU* 1.3 68.4 + - - +
23I GLU* 5.4 1.1 - - + +
30I LEU 3.0 11.4 - - - +
31I TRP* 3.3 21.1 - - - -
32I ASN* 2.8 41.5 + - + +
33I GLN 4.4 2.2 - - - +
34I PRO* 4.3 12.6 - - + -
55I GLU* 4.0 25.1 - - + +
56I THR* 4.1 19.5 - - + -
101I ILE* 5.3 4.9 - - + -
103I CYS 3.9 9.0 - - - +
104I CYS* 3.8 17.5 - - + +
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Residues in contact with GLU 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I VAL* 1.3 86.4 - - - +
23I GLU* 1.3 60.0 + - - +
29I ALA* 3.3 32.3 - - - +
30I LEU 2.9 19.7 - - - +
31I TRP* 4.5 8.7 - - + +
101I ILE* 3.8 5.4 - - - +
102I ASP* 3.2 45.9 + - - +
103I CYS* 3.5 20.9 + - - +
104I CYS* 5.5 0.4 - - - -
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Residues in contact with GLU 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I VAL* 5.4 1.7 - - + +
22I GLU* 1.3 75.1 - - - +
24I THR* 1.3 66.7 + - - +
25I ILE* 3.6 24.5 + - - +
28I LYS 2.9 12.4 - - - +
29I ALA* 4.1 4.3 - - - -
30I LEU* 3.5 13.5 + - - +
100I ASP* 3.2 43.0 - - + +
101I ILE* 4.8 11.5 - - + +
102I ASP* 3.2 4.9 - - - -
119I ARG* 5.7 3.1 + - - -
157I SO4 4.5 13.6 + - - -
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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