Contacts of the strand formed by residues 100 - 106 (chain C) in PDB entry 1YAA
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 VAL 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C ALA* 4.8 0.7 - - + -
88C PHE* 3.7 31.0 - - + -
94C ALA* 3.5 37.5 - - + +
95C LEU* 3.8 21.3 - - + -
98C ASP* 3.3 3.6 - - - +
99C ARG* 1.3 79.8 - - - +
101C ILE* 1.3 66.9 + - - +
102C SER* 3.5 21.3 + - - +
269C LEU* 3.5 13.7 - - - +
280C LYS* 4.3 9.1 - - - +
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Residues in contact with ILE 101 (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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100C VAL* 1.3 71.8 - - - +
102C SER* 1.3 66.5 + - - +
103C VAL* 4.9 4.5 - - + -
269C LEU* 2.8 52.9 - - + +
270C LEU* 4.2 17.0 - - + -
280C LYS* 3.5 47.6 - - + +
283C VAL* 3.9 26.2 - - + -
284C THR* 3.6 17.5 - - + +
287C LEU* 4.0 22.9 - - + -
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Residues in contact with SER 102 (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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74C THR* 4.8 2.1 - - - +
80C THR* 4.0 27.0 + - - +
84C ALA* 3.9 5.9 - - - +
100C VAL* 3.5 14.2 + - - +
101C ILE* 1.3 75.8 - - - +
103C VAL* 1.3 66.2 + - - +
269C PHE* 2.8 38.5 + - - -
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Residues in contact with VAL 103 (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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74C THR* 3.6 33.4 - - + +
80C THR* 3.7 5.8 - - - -
101C ILE* 4.9 6.5 - - + -
102C SER* 1.3 78.8 - - - +
104C GLN* 1.3 62.4 + - - +
114C ILE* 4.6 4.0 - - + -
269C PHE* 2.8 68.3 + - + +
284C THR* 5.3 5.6 - - + -
287C LEU* 4.7 21.1 - - + -
291C ILE* 4.3 22.0 - - + -
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Residues in contact with GLN 104 (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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71C LEU* 3.8 2.4 - - - +
73C ILE 5.0 0.3 - - - +
74C THR 2.9 9.4 + - - +
75C GLY* 3.3 16.4 - - - -
76C LEU* 2.9 26.3 + - - +
79C LEU* 3.9 8.0 - - + +
80C THR* 3.7 9.5 - - + +
103C VAL* 1.3 74.0 - - - +
105C SER* 1.3 66.0 + - - +
266C ARG 5.4 2.6 + - - -
267C VAL* 5.8 2.2 - - - +
268C GLY 3.7 13.7 - - - +
291C ILE* 4.0 19.4 - - - +
298C PRO* 3.5 31.4 - - + +
299C PRO* 3.1 28.9 + - - +
303C ALA* 3.3 23.9 - - - +
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Residues in contact with SER 105 (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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103C VAL 3.7 0.6 + - - -
104C GLN* 1.3 81.1 + - - +
106C LEU* 1.3 59.6 + - - +
107C SER 2.7 34.6 + - - -
110C GLY 3.8 3.4 - - - -
111C ALA* 3.3 32.8 + - - +
114C ILE* 3.8 13.9 - - - -
266C ARG 3.6 3.8 - - - +
268C GLY 3.0 17.7 + - - +
269C PHE 3.4 15.1 + - - -
298C PRO* 5.2 1.6 - - - +
299C PRO* 5.5 0.2 - - - +
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Residues in contact with LEU 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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105C SER* 1.3 72.4 - - - +
107C SER* 1.3 66.0 + - - +
110C GLY* 3.0 24.9 + - - -
266C ARG* 3.8 30.2 + - + -
291C ILE* 6.5 0.7 - - + -
295C VAL* 3.9 30.5 - - + -
298C PRO* 4.6 5.2 - - + -
299C PRO* 3.7 34.8 - - + -
106D LEU* 3.9 19.5 - - + -
295D VAL* 3.9 32.9 - - + +
297D ASN 5.3 0.2 - - - +
299D PRO* 4.6 0.2 - - + -
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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