Contacts of the strand formed by residues 102 - 106 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP* 4.4 16.2 - - - +
85B ASP* 3.7 30.1 - - + -
143B TRP* 5.1 6.2 - - - -
144B THR* 3.8 28.4 - - + +
145B HIS* 5.4 1.8 - - - +
75C SER* 4.7 7.6 - - - +
76C VAL 3.2 9.4 - - - +
77C PRO* 3.4 27.4 - - + -
78C ILE* 3.7 6.9 - - - +
100C PRO* 2.8 21.9 + - + +
101C GLN* 1.3 82.9 - - - +
103C ALA* 1.3 61.3 + - - +
112C LEU 4.7 0.7 - - - +
113C TYR* 3.6 14.4 - - - -
114C MET 5.1 1.7 + - - +
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR* 5.2 1.8 - - - -
58C TRP* 5.4 0.7 - - + -
75C SER* 3.6 3.1 - - - -
76C VAL* 2.8 35.5 + - - +
78C ILE* 3.5 21.0 - - + +
81C LEU* 4.9 7.9 - - + -
102C LEU* 1.3 75.5 - - - +
104C ARG* 1.3 61.0 + - - +
111C VAL* 4.3 15.0 - - + -
112C LEU 3.4 21.5 - - - +
113C TYR* 3.8 6.7 - - + -
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Residues in contact with ARG 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR* 3.8 21.7 + - - +
145B HIS* 4.0 0.2 + - - -
146B HIS* 4.7 13.1 + - - +
149B GLU* 2.9 40.4 + - - -
192B TYR* 4.8 6.5 + - - -
73C GLN* 3.3 50.8 + - + +
74C VAL* 3.1 34.0 - - - +
75C SER* 3.0 23.4 + - - +
103C ALA* 1.3 72.5 - - - +
105C VAL* 1.3 65.7 + - - +
106C VAL* 4.3 0.4 - - + -
110C GLU 3.9 0.3 - - - +
111C VAL* 3.5 0.9 - - - +
112C LEU* 2.8 46.8 + - + +
33G ARG* 4.2 22.1 - - - +
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 4.6 4.3 - - + -
63C LEU* 3.9 25.4 - - + -
65C TRP* 3.4 18.4 - - + -
74C VAL* 2.9 31.6 + - + +
76C VAL* 3.5 29.2 - - + -
81C LEU* 3.7 20.0 - - + -
103C ALA 4.3 1.3 - - - +
104C ARG* 1.3 82.9 - - - +
106C VAL* 1.3 75.4 + - - +
110C GLU 3.4 8.7 - - - +
111C VAL* 4.0 12.8 - - + -
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ALA* 5.1 0.3 - - - -
65C TRP* 3.5 4.5 - - - -
72C ASP* 3.6 15.9 - - + +
73C GLN* 4.0 25.8 - - + +
104C ARG* 5.3 0.4 - - + -
105C VAL* 1.3 88.1 - - - +
107C SER* 1.3 75.4 + - - +
108C ASP* 3.2 24.5 - - + +
109C GLY* 3.3 9.9 + - - -
110C GLU* 2.9 31.2 + - + +
112C LEU* 4.9 9.9 - - + -
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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