Contacts of the strand formed by residues 142 - 148 (chain R) in PDB entry 2YGD
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 142 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78R ASN* 3.6 25.1 - - - +
80R ASP* 3.9 19.7 - - + +
81R VAL 3.7 9.9 - - - +
82R LYS* 4.4 8.5 - - + +
137R LEU* 3.1 8.6 - - - +
138R SER* 2.8 48.6 + - - +
140R ASP* 3.5 28.5 - - + +
141R GLY* 1.3 75.0 - - - +
143R LEU* 1.3 59.7 + - - +
144R THR* 4.3 8.1 - - - +
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Residues in contact with LEU 143 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131Q LEU* 3.6 29.4 - - + -
160Q PRO* 5.7 7.6 - - + -
78R ASN* 3.1 3.0 - - - +
79R LEU* 2.7 47.4 + - + +
86R PRO* 6.6 0.4 - - + -
89R LEU* 4.6 21.1 - - + -
91R VAL* 4.1 24.5 - - + -
100R VAL* 3.8 22.4 - - + -
135R SER* 4.5 0.2 - - - -
136R SER 3.7 5.2 - - - +
137R LEU* 4.2 10.3 - - + -
141R GLY 3.6 1.0 + - - +
142R VAL* 1.3 72.2 - - - +
144R THR* 1.3 71.4 + - - +
145R VAL* 4.2 10.3 - - + -
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Residues in contact with THR 144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R SER* 4.4 9.6 - - - +
77R VAL 3.9 7.2 - - - +
78R ASN* 3.7 16.7 + - + +
135R SER* 3.2 5.7 - - - -
136R SER* 2.8 53.1 + - - +
137R LEU* 4.5 4.3 - - - -
142R VAL* 4.3 8.3 - - - +
143R LEU* 1.3 74.1 - - - +
145R VAL* 1.3 70.7 + - - +
146R ASN* 3.8 15.3 - - + +
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Residues in contact with VAL 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R SER* 3.1 4.9 - - - -
77R VAL* 2.8 52.7 + - + +
79R LEU* 4.2 12.3 - - + -
91R VAL* 5.4 0.2 - - + -
98R ILE* 3.8 27.4 - - + -
128R VAL* 3.7 33.0 - - + -
133R ILE* 3.6 15.7 - - + -
134R THR 3.5 3.4 - - - -
135R SER* 3.4 17.0 - - - +
143R LEU* 4.2 8.9 + - + -
144R THR* 1.3 73.5 - - - +
146R ASN* 1.3 59.8 + - - +
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Residues in contact with ASN 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R PHE 3.6 4.0 - - - -
76R SER* 3.2 21.8 - - - +
133R ILE* 3.5 7.6 - - - +
134R THR* 2.8 56.3 + - - -
135R SER* 3.3 7.6 + - - +
136R SER* 2.5 36.2 + - - -
144R THR* 3.7 8.4 - - + +
145R VAL* 1.3 71.7 - - - +
147R GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74R ARG* 3.9 7.0 - - - -
75R PHE 3.0 33.7 + - - +
76R SER* 4.3 0.2 + - - -
132R THR 4.5 0.9 - - - -
133R ILE* 3.8 2.0 - - - +
134R THR* 4.9 2.5 - - - -
146R ASN* 1.3 75.7 - - - +
148R PRO* 1.4 74.8 - - - +
149R ARG* 3.0 2.1 + - - -
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Residues in contact with PRO 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62R ASP* 3.6 25.6 - - - +
72R LYS* 3.9 5.8 - - + -
73R ASP 3.3 10.5 - - - +
74R ARG* 3.9 15.5 - - + +
132R THR* 2.6 48.4 + - - +
134R THR* 5.8 1.1 - - - +
147R GLY* 1.4 77.5 - - - +
149R ARG* 1.3 60.7 + - - +
166R LYS* 3.7 25.6 - - - +
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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