Contacts of the strand formed by residues 48 - 53 (chain I) in PDB entry 1YKN
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 HIS 48 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40I ALA* 3.9 19.4 + - + +
41I LYS 3.2 29.4 - - - -
42I PRO* 3.5 18.3 + - - +
44I ALA 2.8 22.9 + - - -
46I GLY 3.3 15.9 + - - -
47I GLU* 1.4 72.1 - - - +
49I ILE* 1.3 61.3 + - - +
108I THR 3.6 5.5 + - - +
109I VAL* 3.8 7.7 - - + +
180I LYS* 3.9 29.6 + - + +
181I THR* 4.4 8.8 + - - -
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Residues in contact with ILE 49 (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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47I GLU* 3.6 15.7 - - - +
48I HIS* 1.3 76.7 - - - +
50I LEU* 1.3 56.2 + - - +
51I LEU* 4.4 9.2 - - + -
106I LEU 4.2 0.2 - - - +
107I HIS* 3.9 1.6 - - - -
108I THR* 3.0 50.9 + - + +
109I VAL 3.7 4.9 - - - +
110I LYS* 3.6 33.0 - - + +
145I PHE* 4.2 22.4 - - + -
180I LYS* 4.1 8.0 + - - +
181I THR* 3.5 17.7 - - + +
183I TYR* 4.1 22.4 - - + -
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Residues in contact with LEU 50 (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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49I ILE* 1.3 72.8 - - - +
51I LEU* 1.3 68.5 + - - +
52I LEU* 4.0 20.2 - - + -
105I THR* 4.8 10.3 - - + -
106I LEU 3.6 7.4 - - - +
107I HIS* 3.7 33.4 - - + +
177I VAL* 3.8 37.0 - - + +
180I LYS* 4.1 15.8 - - + +
181I THR 3.0 13.8 + - - +
182I ALA* 3.2 5.6 - - + +
183I TYR 2.9 25.3 + - - -
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Residues in contact with LEU 51 (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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49I ILE* 4.4 3.6 - - + -
50I LEU* 1.3 79.9 - - - +
52I LEU* 1.3 66.8 + - - +
104I TRP* 3.8 15.8 - - + -
105I THR* 3.3 3.5 - - - -
106I LEU* 2.8 55.9 + - + +
108I THR* 4.0 13.2 - - + -
126I ILE* 3.6 28.0 - - + -
143I LEU* 4.0 22.4 - - + -
145I PHE* 4.2 14.6 - - + -
183I TYR* 3.6 29.8 - - + +
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Residues in contact with LEU 52 (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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50I LEU* 4.0 23.8 - - + -
51I LEU* 1.3 79.0 - - - +
53I GLY* 1.3 54.1 + - - +
103I GLU* 4.1 15.3 - - + +
104I TRP* 3.3 21.5 - - - +
105I THR* 4.1 12.1 - - + -
175I CYS* 5.0 3.1 - - - -
177I VAL* 4.3 17.7 - - + -
182I ALA* 4.3 6.1 - - + -
183I TYR 3.0 19.8 + - - +
184I ARG* 3.1 44.6 - - + +
185I PHE* 2.6 32.7 + - - -
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Residues in contact with GLY 53 (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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52I LEU* 1.3 81.8 - - - +
54I GLN* 1.3 62.3 + - - -
103I GLU* 3.2 8.6 - - - +
104I TRP* 2.9 46.0 + - - -
184I ARG* 4.7 2.7 - - - -
185I PHE 3.2 15.0 - - - -
186I ASP* 3.6 5.8 - - - -
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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