Contacts of the strand formed by residues 18 - 22 (chain K) in PDB entry 1S9C
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 PHE 18 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16K PRO 4.0 10.5 - - - +
17K PRO* 1.3 73.7 - - - +
19K SER* 1.3 61.4 + - - +
64K ILE 3.8 6.1 - - - -
65K GLY* 4.0 16.4 - - - -
67K LYS* 3.2 51.1 - - + +
68K SER* 3.5 40.4 - - - +
107K LYS* 3.7 4.2 - - - +
108K CYS* 2.7 70.0 + - + +
110K ALA* 4.6 14.4 - - + -
128K VAL* 4.5 4.0 - - + -
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Residues in contact with SER 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K PHE* 1.3 85.6 - - - +
20K TYR* 1.3 63.4 + - - +
67K LYS* 4.2 12.8 + - - +
105K LYS* 6.5 0.4 - - - -
106K LEU 3.1 15.9 - - - -
107K LYS* 4.2 6.3 - - - -
108K CYS 4.2 0.7 - - - +
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Residues in contact with TYR 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K SER* 1.3 74.6 - - - +
21K ALA* 1.3 66.3 + - - +
22K TYR* 3.6 28.5 - + + -
26K GLU* 4.3 14.9 - - - +
60K PHE* 3.9 15.4 - + - -
63K ILE* 3.6 25.9 - - + +
64K ILE* 3.7 46.7 - - + +
67K LYS* 4.1 26.2 - - + -
104K GLY 4.1 0.5 - - - +
105K LYS 3.4 0.5 - - - -
106K LEU* 2.6 44.3 + - + +
108K CYS* 4.3 3.7 - - - -
191K SER 5.2 1.8 + - - -
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Residues in contact with ALA 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K SER 4.4 0.2 - - - -
20K TYR* 1.3 86.0 - - - +
22K TYR* 1.3 64.0 + - - +
26K GLU* 5.1 2.6 - - - +
104K GLY 3.3 4.9 - - - -
105K LYS* 3.3 33.2 - - + -
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Residues in contact with TYR 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K TYR* 3.6 28.5 - + + -
21K ALA* 1.3 76.6 - - - +
23K THR* 1.3 80.3 + - - +
26K GLU* 3.7 22.2 - - + -
27K ALA* 5.0 1.8 - - + -
56K CYS* 4.6 3.4 - - - -
60K PHE* 3.6 27.4 - + + -
64K ILE* 3.8 3.9 - - + +
100K LEU* 4.3 6.2 - - - +
101K PRO* 3.0 41.6 + - + +
102K ARG 4.2 1.8 - - - -
103K ALA* 3.3 26.0 - - - +
104K GLY 2.8 38.8 + - - +
106K LEU* 3.8 23.9 - - + +
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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