Contacts of the strand formed by residues 101 - 107 (chain L) in PDB entry 1KYO
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 GLN 101 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53L VAL* 3.3 7.1 - - - +
54L PHE* 2.8 33.3 + - + +
56L SER* 3.0 20.3 + - - +
57L GLY* 3.9 3.0 - - - -
69L SER* 3.1 35.2 + - - -
72L TRP* 4.3 0.2 - - - +
95L ASN 3.6 6.3 - - - -
96L ILE* 3.5 18.6 - - + +
100L PHE* 1.3 76.6 - - - +
102L SER* 1.3 62.1 + - - +
103L TYR* 2.8 29.7 + - + -
195L PHE* 3.8 12.1 - - - -
200L PHE* 3.2 24.6 - - + -
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Residues in contact with SER 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L VAL 3.6 4.5 - - - -
53L VAL* 3.7 21.5 - - - -
93L SER 5.1 0.3 + - - -
94L SER* 3.1 9.9 + - - -
95L ASN* 2.9 46.7 + - - +
100L PHE* 4.5 0.4 - - - -
101L GLN* 1.3 78.7 - - - +
103L TYR* 1.3 65.8 + - - +
104L ILE* 4.1 8.7 - - - +
387L ASN* 2.9 32.1 + - - -
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Residues in contact with TYR 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L GLY* 3.1 2.3 - - - -
52L VAL* 2.9 35.6 + - - +
54L PHE* 3.9 19.5 - + - -
69L SER 4.0 1.4 + - - -
72L TRP* 3.0 26.1 - + + +
73L LYS* 3.6 8.8 + - - -
76L PHE* 3.4 47.6 - + + -
93L SER 4.0 1.8 - - - -
94L SER* 3.4 20.9 - - - -
96L ILE* 4.1 0.9 - - + +
101L GLN* 2.8 41.6 + - + +
102L SER* 1.3 72.5 - - - +
104L ILE* 1.3 60.9 + - - +
119L LEU* 4.2 3.2 - - - +
123L PHE* 3.4 36.3 - + + -
200L PHE* 4.2 5.4 - + - -
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Residues in contact with ILE 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L SER* 3.8 26.7 - - - -
50L VAL 3.9 6.7 - - - +
51L GLY* 3.9 12.1 - - - -
53L VAL* 4.9 4.7 - - + -
76L PHE* 4.4 2.4 - - - -
91L ALA 3.7 0.3 - - - +
92L LEU* 3.5 3.3 - - - -
93L SER* 2.7 51.3 + - - +
102L SER* 4.5 9.2 - - - +
103L TYR* 1.3 82.2 - - - +
105L VAL* 1.3 67.7 + - - +
106L SER* 4.7 0.4 - - - +
383L VAL* 4.2 17.0 - - + +
386L ALA* 3.4 30.5 - - + -
387L ASN* 4.1 23.1 - - - +
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Residues in contact with VAL 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L SER* 3.4 2.4 - - - -
50L VAL* 2.9 41.2 + - - +
76L PHE* 4.2 6.5 - - + -
90L LEU* 3.6 38.8 - - + -
91L ALA 3.3 4.5 - - - +
92L LEU* 3.5 24.5 - - + -
104L ILE* 1.3 75.4 - - - +
106L SER* 1.3 63.8 + - - +
115L SER* 3.9 18.2 + - - +
118L PHE* 4.0 10.3 - - + -
119L LEU* 3.4 25.1 - - + -
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Residues in contact with SER 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L THR* 5.4 5.2 - - - -
49L SER* 2.7 23.1 + - - -
90L LEU* 3.2 10.0 - - - +
91L ALA* 2.6 51.3 + - - +
93L SER* 4.4 2.6 + - - -
104L ILE* 4.8 0.5 - - - +
105L VAL* 1.3 72.8 - - - +
107L SER* 1.3 62.8 + - - +
383L VAL* 3.2 21.7 - - - +
323M LEU* 4.7 7.1 - - - +
327M VAL* 6.2 2.0 - - - -
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Residues in contact with SER 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L THR* 3.2 5.9 - - - -
48L ALA* 3.0 39.0 + - - +
50L VAL* 5.6 1.0 + - - +
89L GLY 4.3 2.9 - - - -
90L LEU* 3.8 15.9 - - - -
106L SER* 1.3 77.2 - - - +
108L LEU* 1.3 67.2 + - - +
111L SER* 4.0 12.2 + - - -
112L THR* 4.5 3.1 - - - -
115L SER* 2.9 24.8 + - - -
323M LEU* 3.4 15.4 - - - +
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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