Contacts of the strand formed by residues 67 - 71 (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 PHE 67 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I VAL* 4.3 20.6 - - + -
18I HIS* 4.7 3.6 - + + -
21I LEU* 3.5 56.1 - - + -
22I ALA* 4.4 9.2 - - + -
36I TRP* 4.6 0.7 - + - -
66I SER* 1.3 75.0 - - - +
68I LEU* 1.3 60.3 + - - +
69I GLU* 3.7 22.0 - - + -
94I ARG* 3.4 41.3 - - + -
95I THR 3.7 12.3 - - - -
96I ALA* 4.4 7.9 - - + -
130I LEU* 3.7 3.3 - - - +
131I PHE* 2.9 56.8 + + + +
475J ILE* 5.0 1.3 - - + -
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Residues in contact with LEU 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I VAL* 4.7 1.8 - - + -
66I SER* 3.8 19.7 - - - +
67I PHE* 1.3 80.6 - - - +
69I GLU* 1.4 64.8 + - - +
70I VAL* 5.1 3.6 - - + -
94I ARG* 3.2 7.1 - - - +
95I THR* 2.9 47.4 + - + +
96I ALA* 4.7 1.8 - - - -
104I TRP* 3.8 53.6 - - + +
128I ILE* 4.0 22.0 - - + -
129I SER 3.3 8.3 - - - +
130I LEU* 4.1 15.0 - - + -
187I ILE* 4.6 7.6 - - + -
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Residues in contact with GLU 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I PHE* 3.7 16.0 - - + -
68I LEU* 1.4 74.9 - - - +
70I VAL* 1.4 62.8 + - - +
92I PHE* 3.7 22.3 - - + -
93I GLY 3.6 3.8 - - - -
94I ARG* 2.6 49.1 + - - -
128I ILE* 3.3 5.7 - - - +
129I SER* 2.9 37.0 + - - +
131I PHE* 4.2 10.0 - - + -
473J LYS* 3.1 37.9 + - - +
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Residues in contact with VAL 70 (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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39I LEU* 4.3 12.6 - - + -
68I LEU* 5.1 8.1 - - + -
69I GLU* 1.4 80.9 - - - +
71I TRP* 1.3 61.1 + - - +
72I GLN* 5.7 0.9 - - + +
91I SER 4.1 0.2 - - - -
92I PHE* 3.3 12.2 - - - -
93I GLY* 3.0 41.3 + - - +
95I THR* 5.4 2.9 - - + -
104I TRP* 6.1 0.7 - - + -
106I LEU* 3.7 35.4 - - + -
126I ILE* 4.1 11.7 - - + -
127I ASN 3.1 6.5 - - - +
128I ILE* 4.0 23.1 - - + -
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Residues in contact with TRP 71 (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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70I VAL* 1.3 75.7 - - - +
72I GLN* 1.4 60.5 + - - +
79I TYR* 3.2 36.9 - + + -
80I GLN 4.2 2.5 - - - -
81I ASP* 3.9 19.3 - - + -
91I SER* 3.2 39.9 - - - -
92I PHE* 3.8 11.2 - + + -
127I ASN* 2.9 43.3 + - + +
344J SER 3.3 23.8 + - - -
347J THR* 3.1 32.7 + - - -
348J GLY* 3.3 25.8 - - - -
349J PRO* 3.4 27.1 - - + -
470J ILE* 3.7 28.3 - - + -
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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