Contacts of the strand formed by residues 145 - 154 (chain A) in PDB entry 2YD0
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 TYR 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A GLU* 3.3 5.6 - - - +
84A ILE* 2.9 43.3 + - + -
85A THR* 5.3 2.2 - - - -
86A ALA 5.6 1.1 - - - -
107A LEU* 3.8 32.1 - - + -
108A ARG 3.3 16.4 - - - +
109A LYS* 4.3 15.9 - - + -
110A GLY 4.0 2.0 - - - -
138A PRO 4.0 2.9 + - - -
139A LEU* 3.4 26.7 - - + -
140A LEU* 2.7 49.1 + - - +
143A LEU* 3.4 31.8 - - + +
144A PRO* 1.3 77.7 - - - +
146A THR* 1.3 62.5 + - - +
147A VAL 4.2 0.2 - - - -
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Residues in contact with THR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LYS* 4.1 16.8 - - + -
82A VAL 3.6 10.1 - - - +
83A GLU* 3.6 18.0 - - + +
106A THR 3.8 0.5 - - - +
107A LEU* 3.5 2.9 - - - +
108A ARG* 2.8 54.5 + - - +
110A GLY 3.5 11.5 + - - -
145A TYR* 1.3 75.0 + - - +
147A VAL* 1.3 68.1 + - - +
148A VAL* 3.9 20.4 + - + +
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A THR 3.8 1.2 - - - +
81A LYS* 3.3 3.6 - - - -
82A VAL* 2.9 45.9 + - + +
84A ILE* 3.6 32.8 - - + -
93A ILE* 3.8 11.7 - - + -
95A LEU* 5.3 2.0 - - + -
106A THR 3.4 8.5 - - - +
107A LEU* 3.8 16.8 - - + -
120A LEU* 4.5 2.9 - - + -
133A LEU* 3.5 28.3 - - + -
146A THR* 1.3 73.0 - - - +
148A VAL* 1.3 60.8 + - - +
149A ILE* 3.9 17.7 - - + -
194A PHE* 6.1 0.7 - - + -
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A THR* 4.4 7.0 - - + -
80A THR 3.4 3.6 - - - +
81A LYS* 3.8 30.5 - - + -
104A ARG 3.8 0.9 - - - +
105A ALA* 3.2 4.0 - - - -
106A THR* 2.9 48.4 + - - +
108A ARG* 3.8 33.9 - - - +
146A THR* 3.9 13.5 - - + +
147A VAL* 1.3 78.3 - - - +
149A ILE* 1.3 63.2 + - - +
150A HIS* 4.1 22.8 - - + +
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A THR* 3.3 3.8 - - - +
80A THR* 2.8 43.1 + - + +
82A VAL* 5.7 1.8 - - + -
95A LEU* 4.1 15.5 - - + -
102A ILE* 3.8 39.9 - - + -
104A ARG 3.4 3.1 - - - -
105A ALA* 4.4 9.0 - - + -
131A ILE* 4.4 6.7 - - + -
133A LEU* 4.2 7.2 - - + -
147A VAL* 3.9 22.9 - - + +
148A VAL* 1.3 78.1 - - - +
150A HIS* 1.3 66.6 + - - +
151A TYR* 3.9 3.9 - - + -
192A PRO* 3.8 33.9 - - + +
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Residues in contact with HIS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A GLY 3.4 4.7 - - - +
79A THR* 3.0 37.9 + - + +
102A ILE* 3.7 3.3 - - - +
103A SER* 3.0 33.3 + - - +
104A ARG* 3.0 42.6 + - + +
106A THR* 5.9 2.0 + - + -
108A ARG* 6.1 0.2 + - - -
148A VAL* 4.1 16.1 - - + +
149A ILE* 1.3 72.7 - - - +
151A TYR* 1.3 62.5 + - - +
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Residues in contact with TYR 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU 4.6 0.7 + - - -
67A ILE* 3.6 14.0 - - - +
76A PHE* 4.1 9.0 - + - -
77A TRP* 3.5 5.8 - - - +
78A GLY* 2.9 52.3 + - - +
79A THR 3.9 0.7 - - - -
80A THR* 3.5 20.6 + - - -
100A LEU* 3.8 28.9 - - + -
101A GLN 3.2 16.2 - - - +
102A ILE* 3.7 18.2 - - + -
103A SER* 4.2 5.6 + - - -
149A ILE* 3.9 9.2 - - + -
150A HIS* 1.3 77.8 - - - +
152A ALA* 1.3 66.2 + - - +
190A ALA 2.6 29.7 + - - -
191A PHE* 3.2 11.4 - - - +
192A PRO* 3.6 13.2 - - + -
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Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A THR* 5.4 3.1 - - + -
76A PHE 3.2 12.6 - - - +
77A TRP* 3.7 20.9 - - + +
100A LEU* 3.6 3.8 - - - -
101A GLN* 2.9 38.0 + - + +
151A TYR* 1.3 84.0 - - - +
153A GLY* 1.3 60.3 + - - +
1C NAG 4.0 2.1 - - - +
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Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A THR* 3.3 9.5 - - - +
76A PHE* 2.7 55.8 + - - +
99A HIS 4.7 1.6 - - - -
100A LEU* 4.5 5.2 - - - -
152A ALA* 1.3 75.5 - - - +
154A ASN* 1.3 62.2 + - - -
1C NAG 4.4 11.0 - - - -
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Residues in contact with ASN 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU 3.6 11.1 - - - +
75A THR* 4.0 10.2 + - - +
76A PHE* 3.5 10.2 - - - -
99A HIS 5.3 1.0 + - - -
153A GLY* 1.3 76.8 - - - +
155A LEU* 1.3 71.5 - - - +
156A SER* 3.2 3.6 + - - -
1C NAG 1.4 64.5 + - - +
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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