Contacts of the strand formed by residues 102 - 106 (chain D) in PDB entry 1YI5
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 LEU 102 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ASP* 4.3 9.6 - - - +
85C ASP* 3.8 27.8 - - + -
143C TRP* 5.0 5.4 - - - -
144C THR* 3.8 30.3 - - + +
145C HIS* 5.2 3.8 - - - +
75D SER* 4.4 11.7 - - - +
76D VAL 3.2 15.9 - - - +
77D PRO* 3.4 20.4 - - + -
78D ILE* 3.7 6.2 - - - +
100D PRO* 2.8 21.0 + - + +
101D GLN* 1.3 82.0 - - - +
103D ALA* 1.3 61.2 + - - +
112D LEU 4.6 0.7 - - - +
113D TYR* 3.9 13.2 - - - -
114D MET 5.1 1.6 + - - +
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Residues in contact with ALA 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C THR* 5.0 2.5 - - - -
58D TRP* 5.4 0.9 - - + -
75D SER* 3.6 2.3 - - - -
76D VAL* 2.8 41.2 + - - +
78D ILE* 3.6 19.7 - - + +
81D LEU* 4.5 15.0 - - + -
102D LEU* 1.3 74.6 - - - +
104D ARG* 1.3 63.1 + - - +
105D VAL* 4.5 0.4 - - - -
111D VAL* 4.5 5.4 - - + -
112D LEU 3.3 21.8 - - - +
113D TYR* 3.8 8.3 - - + -
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Residues in contact with ARG 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C THR* 3.0 34.5 + - + +
145C HIS* 3.9 1.2 - - - +
146C HIS* 3.5 20.2 + - - +
149C GLU* 3.3 30.1 + - - -
188C CYS* 6.2 0.4 - - - +
192C TYR* 4.8 5.8 + - - -
73D GLN* 3.5 52.5 + - + +
74D VAL 3.7 11.3 - - - +
75D SER* 3.0 22.0 + - - +
103D ALA* 1.3 72.0 - - - +
105D VAL* 1.3 65.8 + - - +
111D VAL* 3.5 0.9 - - - +
112D LEU* 2.8 58.5 + - + +
33H ARG* 4.4 17.7 - - - +
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ILE* 4.3 7.4 - - + -
63D LEU* 3.9 23.8 - - + -
65D TRP* 3.3 27.2 - - + -
73D GLN* 3.9 2.4 - - - -
74D VAL* 2.9 25.3 + - + +
76D VAL* 3.3 30.7 - - + -
81D LEU* 3.9 21.5 - - + -
103D ALA 4.1 0.9 - - - +
104D ARG* 1.3 79.6 - - - +
106D VAL* 1.3 71.4 + - - +
110D GLU 3.5 7.6 - - - +
111D VAL* 4.3 9.6 - - + -
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Residues in contact with VAL 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D TRP* 3.2 11.8 - - - -
72D ASP* 3.6 15.9 - - + +
73D GLN* 4.1 24.9 - - + +
105D VAL* 1.3 81.0 - - - +
107D SER* 1.3 76.5 + - - +
108D ASP* 3.2 21.5 - - + +
109D GLY* 3.3 10.4 + - - -
110D GLU* 2.9 30.3 + - + +
112D LEU* 4.5 12.8 - - + -
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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