Contacts of the strand formed by residues 104 - 108 (chain K) in PDB entry 1I9R
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 ASP 104 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K SER* 3.6 1.0 - - - -
100K ASP* 2.8 67.4 + - - +
103K ASN* 1.3 80.2 - - - +
105K MET* 1.3 58.9 + - - +
106K ASP* 3.4 1.9 + - - +
499K ZN 3.2 11.1 - - - -
38M HIS* 3.8 11.5 + - + +
40M TYR* 3.9 6.3 - - - +
50M LEU* 3.6 21.9 - - + +
53M LYS* 3.4 26.1 - - + -
54M TYR* 3.4 18.0 + - - -
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Residues in contact with MET 105 (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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35K TYR* 3.7 25.1 - - + -
37K VAL* 3.3 29.2 - - + -
47K TRP* 4.8 3.6 - - - -
97K THR* 3.5 16.8 - - + +
98K ARG 3.6 8.7 - - - +
99K SER* 4.1 3.6 - - - +
103K ASN 4.1 2.7 - - - +
104K ASP* 1.3 70.8 - - - +
106K ASP* 1.3 57.8 + - - +
107K SER 3.7 1.3 - - - -
108K TRP* 3.1 44.7 + - + -
40M TYR* 3.0 30.1 + - + +
50M LEU* 4.4 1.7 - - - +
93M GLN* 3.5 19.5 - - - +
100M PRO* 5.0 2.0 - - - -
102M PHE* 3.6 16.4 - - + -
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Residues in contact with ASP 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98K ARG* 2.6 51.9 + - - +
100K ASP* 3.5 9.4 - - - +
104K ASP* 3.4 8.9 + - - +
105K MET* 1.3 71.5 - - - +
107K SER* 1.3 68.5 + - - -
108K TRP* 4.5 2.0 - - - -
499K ZN 2.4 34.8 - - - -
49M LYS* 4.9 5.7 + - - -
50M LEU* 3.9 14.4 - - + +
59M GLU* 3.6 14.9 - - - +
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Residues in contact with SER 107 (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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2K VAL* 4.1 30.8 - - - +
3K GLN* 5.9 0.2 - - - -
4K LEU* 3.7 10.3 - - - +
97K THR* 2.6 27.4 + - - -
98K ARG* 3.0 21.1 + - - -
105K MET 3.7 3.2 + - - -
106K ASP* 1.3 97.7 + - - +
108K TRP* 1.3 62.7 + - - +
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Residues in contact with TRP 108 (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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4K LEU* 4.1 9.7 + - - +
37K VAL* 3.8 22.2 - - + -
45K LEU* 4.9 1.6 - - + -
95K TYR* 3.5 29.4 - + + -
96K CYS 3.5 4.0 - - - +
97K THR* 3.6 9.4 + - + -
105K MET* 3.1 48.3 + - + -
106K ASP 4.5 1.1 - - - -
107K SER* 1.3 88.8 - - - +
109K GLY* 1.3 71.3 + - - +
40M TYR* 4.0 14.8 - + - -
47M PRO* 3.8 13.8 - - + +
48M PRO* 3.6 59.7 + - + +
49M LYS* 5.6 1.1 - - - -
50M LEU 5.4 1.2 - - - +
102M PHE* 3.9 11.4 - + - -
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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