Contacts of the strand formed by residues 144 - 157 (chain A) in PDB entry 3DOY
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 LYS 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ILE* 4.2 24.2 - - + -
140A GLN* 3.2 4.9 - - - -
141A VAL 2.9 32.6 + - - +
142A ASP* 4.3 19.1 + - - +
143A GLY* 1.3 80.8 - - - +
145A VAL* 1.3 63.9 + - - +
146A VAL* 3.3 3.3 + - + +
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Residues in contact with VAL 145 (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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110A ARG* 3.6 29.3 - - - +
111A ILE* 3.8 9.0 - - - +
138A THR* 4.0 15.0 - - + +
139A ALA 3.7 3.6 - - - -
140A GLN* 4.1 17.3 - - + +
143A GLY 5.3 1.8 - - - +
144A LYS* 1.3 72.9 - - - +
146A VAL* 1.3 57.9 + - - +
147A ALA 3.4 25.4 - - - +
148A GLU* 4.0 19.7 - - + +
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Residues in contact with VAL 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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70A ILE* 4.7 2.6 - - + +
109A PHE* 3.7 2.6 - - - +
110A ARG* 2.8 24.9 + - - -
111A ILE* 3.2 44.4 + - + +
112A PRO 5.3 0.4 - - - +
113A VAL* 3.8 21.3 - - + -
119A LEU* 4.0 5.2 - - + -
139A ALA* 2.8 33.3 + - + +
141A VAL* 3.6 27.1 - - + +
144A LYS* 3.7 10.8 - - + +
145A VAL* 1.3 74.4 - - - +
147A ALA* 1.3 63.8 + - + +
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Residues in contact with ALA 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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70A ILE* 4.0 16.2 - - + -
71A VAL* 6.2 0.9 - - + -
74A MET* 5.1 3.6 - - - -
107A VAL* 6.1 0.2 - - + -
108A LYS 3.1 12.1 - - - +
109A PHE* 4.2 16.4 - - + -
110A ARG* 4.4 0.7 - - - +
138A THR* 3.3 9.4 - - - -
139A ALA* 2.9 39.7 + - + -
145A VAL* 3.4 4.4 - - - +
146A VAL* 1.3 85.9 - - + +
148A GLU* 1.3 64.6 + - - +
149A ALA* 6.3 0.2 - - + -
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Residues in contact with GLU 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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74A MET* 4.6 0.7 - - - -
106A LYS 3.8 7.5 - - - +
107A VAL* 3.0 6.9 - - - +
108A LYS* 2.8 44.9 + - + +
110A ARG* 2.7 42.5 + - - +
137A GLY 3.7 7.4 - - - +
138A THR* 4.0 10.3 - - + +
145A VAL* 4.0 12.4 - - + +
147A ALA* 1.3 79.9 - - - +
149A ALA* 1.3 64.4 + - - +
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Residues in contact with ALA 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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71A VAL* 4.5 12.1 - - + -
74A MET* 3.6 24.2 - - + +
104A ILE* 5.1 0.2 - - + -
105A ASP 4.0 1.6 - - - -
106A LYS 3.8 8.4 + - - -
107A VAL* 4.0 15.5 - - + +
123A LEU* 5.3 0.6 - - - +
136A GLY* 3.5 1.4 - - - -
137A GLY 3.0 33.9 + - - +
148A GLU* 1.3 77.6 - - - +
150A GLU* 1.3 63.8 + - - +
151A LEU* 4.9 9.4 - - + -
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Residues in contact with GLU 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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104A ILE* 3.3 4.0 - - - +
105A ASP* 2.8 45.6 + - + +
106A LYS* 3.3 42.6 + - + +
126A LEU* 4.4 18.1 - - + +
134A GLN* 6.4 1.6 - - + -
135A VAL 3.4 12.1 - - - +
136A GLY* 4.0 3.3 - - - -
149A ALA* 1.3 78.0 - - - +
151A LEU* 1.3 71.9 + - - +
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Residues in contact with LEU 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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71A VAL* 4.8 10.8 - - + +
74A MET* 4.9 4.9 - - + -
75A ALA* 4.2 28.0 - - + +
78A GLY* 6.0 0.2 - - - -
101A PHE* 3.8 31.0 - - + -
103A THR* 3.1 18.8 - - - +
104A ILE* 4.2 2.2 - - + -
105A ASP* 4.9 0.9 - - - +
123A LEU* 5.2 3.1 - - + -
133A TRP 3.9 0.2 - - - +
134A GLN* 3.4 2.5 - - - +
135A VAL* 2.7 62.4 + - + +
149A ALA* 4.9 7.0 - - + -
150A GLU* 1.3 85.4 - - - +
152A LYS* 1.3 64.6 + - - +
153A ALA* 4.6 10.1 - - + -
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Residues in contact with LYS 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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101A PHE* 3.9 1.4 - - - -
102A MET* 2.9 65.8 + - - +
103A THR* 3.2 32.1 + - - +
132A ILE* 4.0 20.4 - - + +
133A TRP 3.2 5.6 - - - +
134A GLN* 3.4 33.4 - - + +
151A LEU* 1.3 76.9 - - - +
153A ALA* 1.3 61.7 + - - +
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Residues in contact with ALA 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 ALA 6.1 0.7 - - - +
78A GLY 6.4 0.4 - - - -
79A GLY* 6.0 2.0 - - - +
99A VAL* 3.6 21.1 - - + -
100A TYR 3.2 12.8 - - - +
101A PHE* 5.0 1.1 - - + -
102A MET* 4.1 7.9 - - - +
131A MET 4.4 0.2 - - - -
132A ILE* 3.7 5.2 - - - +
133A TRP* 2.6 42.6 + - + +
135A VAL* 6.4 0.2 - - + -
151A LEU* 4.2 13.4 - - + +
152A LYS* 1.3 75.6 - - - +
154A MET* 1.3 62.6 + - - +
155A ILE* 5.9 0.7 - - + -
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Residues in contact with MET 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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98A ILE 3.5 1.7 - - - +
99A VAL* 3.1 5.6 - - - -
100A TYR* 2.7 51.4 + - + +
102A MET* 3.8 38.1 - - + -
131A MET 3.5 4.9 - - - -
132A ILE* 4.4 4.3 - - + -
153A ALA* 1.3 76.4 - - - +
155A ILE* 1.3 65.1 + - - +
156A ALA* 4.2 10.8 - - + -
2005A BEN 3.3 52.7 - - + -
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Residues in contact with ILE 155 (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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82A ALA* 4.0 13.9 - - + -
83A PHE* 4.2 8.1 - - + +
86A LEU* 3.4 33.2 - - + -
87A TRP* 4.0 19.3 - - + -
97A LYS* 3.9 32.4 + - + -
98A ILE 3.7 4.0 - - - +
99A VAL* 4.1 17.7 - - + +
131A MET* 3.0 40.8 + - - +
133A TRP* 4.0 15.0 - - + +
153A ALA* 5.9 0.7 - - + -
154A MET* 1.3 72.6 - - - +
156A ALA* 1.3 60.2 + - - +
2005A BEN 3.8 6.2 - - - -
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Residues in contact with ALA 156 (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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97A LYS* 3.2 14.4 - - - +
98A ILE* 2.8 37.3 + - + +
100A TYR* 4.0 24.0 - - + -
154A MET* 3.6 12.7 + - + -
155A ILE* 1.3 74.8 - - - +
157A GLU* 1.3 67.1 + - - +
2005A BEN 4.3 12.1 - - + -
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Residues in contact with GLU 157 (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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96A THR* 3.7 10.9 + - - +
97A LYS* 2.8 36.3 + - - +
98A ILE* 3.8 8.3 - - - +
100A TYR* 5.0 3.5 + - - -
156A ALA* 1.3 81.5 - - - +
158A ARG* 1.3 62.5 + - - +
159A GLU 3.2 18.1 + - - +
2005A BEN 5.7 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