Contacts of the strand formed by residues 75 - 79 (chain U) 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 PHE 75 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67U GLU* 3.7 18.4 - - - -
69U ARG 3.2 18.8 - - - -
70U LEU* 3.7 13.7 - - + +
72U LYS 3.2 6.2 + - - +
74U ARG* 1.3 73.7 - - - +
76U SER* 1.3 61.8 + - - +
77U VAL* 3.2 34.1 - - + -
124U ILE* 4.8 1.6 - - + -
127U ASP* 3.6 34.5 - - + -
128U VAL* 4.8 3.1 - - + -
133U ILE* 4.2 9.6 - - + -
145U VAL* 5.7 1.3 - - + -
146U ASN* 3.3 2.8 - - - -
147U GLY 2.8 36.7 + - - +
149U ARG* 3.1 53.4 - - + +
111X HIS* 4.4 10.1 - + - -
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Residues in contact with SER 76 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65U LEU 4.5 4.3 - - - -
66U SER 3.4 17.4 - - - +
67U GLU* 3.6 8.7 - - - -
69U ARG* 3.1 39.2 + - - +
74U ARG* 3.9 4.7 + - - +
75U PHE* 1.3 83.3 + - - +
77U VAL* 1.3 67.5 + - - +
144U THR* 4.1 13.2 - - - +
145U VAL 3.2 9.6 - - - -
146U ASN* 3.4 15.1 - - - +
163V ARG* 6.0 0.3 - - - +
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Residues in contact with VAL 77 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66U SER* 3.8 5.2 - - - -
75U PHE* 3.2 41.5 - - + -
76U SER* 1.3 73.5 - - - +
78U ASN* 1.3 59.3 + - - +
79U LEU* 3.7 10.2 - - + +
122U TYR* 3.2 43.3 - - + +
124U ILE* 4.4 7.4 - - + -
144U THR* 3.3 4.5 - - - -
145U VAL* 2.8 52.5 + - + +
111X HIS* 4.1 14.4 - - + +
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Residues in contact with ASN 78 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64U GLY* 3.2 25.9 + - - +
65U LEU 3.7 5.4 - - - +
66U SER* 3.5 34.0 + - - +
77U VAL* 1.3 71.8 - - - +
79U LEU* 1.3 57.2 + - - +
80U ASP* 3.4 20.4 - - - +
120U ARG* 3.1 26.0 + - - +
122U TYR* 4.5 0.7 - - - -
142U VAL* 3.1 32.3 - - - +
143U LEU 3.7 2.7 - - - -
144U THR* 3.2 12.3 + - - +
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Residues in contact with LEU 79 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77U VAL* 3.7 28.3 - - + +
78U ASN* 1.3 68.8 - - - +
80U ASP* 1.3 65.4 + - - +
81U VAL 3.6 0.3 + - - -
98U ILE* 4.1 14.8 - - + +
100U VAL* 3.9 29.7 - - + +
120U ARG* 3.8 24.0 - - + +
122U TYR* 3.3 36.8 - - + -
141U GLY 4.4 0.5 - - - +
143U LEU* 2.7 42.4 + - + +
145U VAL* 4.1 20.2 - - + -
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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