Contacts of the helix formed by residues 83 - 88 (chain K) in PDB entry 3SWD
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 PRO 83 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56K LEU* 5.5 1.1 - - + -
59K GLN* 3.7 28.5 - - + +
81K CYS* 3.3 16.8 - - - +
82K ALA* 1.3 86.1 - - - +
84K TYR* 1.3 67.3 + - - +
85K ASP* 3.1 9.4 - - + +
86K LEU* 2.8 27.8 + - + +
87K VAL 3.1 9.7 + - - -
110K SER* 4.2 0.7 - - - -
142K TYR* 3.6 15.9 - - + +
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Residues in contact with TYR 84 (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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83K PRO* 1.3 70.2 - - - +
85K ASP* 1.3 60.7 + - - +
88K LYS* 2.9 71.0 + - + +
110K SER* 3.4 16.6 - - - +
142K TYR* 3.1 18.4 + - + +
337L GLU* 4.5 2.1 + - - -
340L ARG* 3.1 37.0 - - - -
364L GLN* 3.0 72.6 + - + +
365L VAL* 3.8 13.3 + - - -
366L MET* 4.0 9.9 + - - +
390L ASP* 5.8 1.6 - - + +
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Residues in contact with ASP 85 (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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83K PRO* 3.0 8.8 + - + +
84K TYR* 1.3 78.4 - - - +
86K LEU* 1.3 66.0 + - + +
88K LYS* 3.8 17.7 + - - +
89K THR* 3.6 18.2 - - - +
364L GLN* 4.8 12.4 + - - -
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Residues in contact with LEU 86 (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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52K THR* 4.2 15.1 - - + +
55K LYS* 3.3 33.0 - - + +
56K LEU* 3.2 58.8 - - + +
59K GLN* 3.9 20.9 - - - +
83K PRO* 2.8 16.8 + - + +
85K ASP* 1.3 83.7 - - + +
87K VAL* 1.3 62.0 + - - +
88K LYS 3.3 1.1 - - - -
89K THR* 2.3 29.6 + - + +
90K MET 3.4 2.4 + - - -
93K SER* 4.2 5.8 + - - -
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Residues in contact with VAL 87 (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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82K ALA* 3.6 17.9 - - + +
83K PRO 3.1 4.8 + - - +
84K TYR 4.1 0.2 - - - +
86K LEU* 1.3 74.4 - - + +
88K LYS* 1.3 58.6 + - - +
90K MET 2.6 44.9 + - - +
91K ARG* 3.7 4.3 + - + +
93K SER* 4.0 17.9 - - - -
94K ILE 5.4 1.1 - - - +
109K VAL* 4.2 5.4 - - + -
110K SER* 3.6 51.4 - - - +
112K PRO* 4.2 22.2 - - + -
115K QPA 4.9 0.2 + - - -
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Residues in contact with LYS 88 (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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84K TYR* 2.9 57.3 + - + +
85K ASP* 3.8 19.7 + - - +
87K VAL* 1.3 77.8 - - - +
89K THR* 1.3 67.3 + - + +
115K QPA 4.3 11.3 + - - -
3L LYS* 5.9 0.8 - - - +
366L MET* 3.4 29.1 - - + +
390L ASP* 3.2 28.7 + - - +
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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