Contacts of the strand formed by residues 99 - 108 (chain A) in PDB entry 2BQY
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 GLY 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A GLU* 4.2 7.2 - - - -
96A ASP* 2.9 37.5 + - - +
98A SER* 1.3 80.2 - - - +
100A MET* 1.3 67.0 + - - -
101A ASP 3.4 0.7 + - - -
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Residues in contact with MET 100 (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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63A SER* 3.8 25.3 - - - +
64A ASP* 5.4 2.4 + - - +
93A ASN* 5.7 4.3 - - + -
94A MET 3.2 26.5 - - - +
95A GLU* 3.4 27.1 - - + +
99A GLY* 1.3 73.0 - - - -
101A ASP* 1.3 60.8 + - - +
102A GLU* 5.1 8.3 - - + -
152A LYS* 4.3 16.4 - - - +
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Residues in contact with ASP 101 (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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63A SER* 5.5 0.4 - - - -
64A ASP* 5.2 10.1 - - - +
69A ASP* 4.3 4.9 - - - +
93A ASN* 3.8 3.1 - - - +
94A MET* 2.8 51.9 + - + +
96A ASP* 4.0 22.3 - - - +
99A GLY 3.4 1.9 + - - +
100A MET* 1.3 74.7 - - - +
102A GLU* 1.3 77.7 + - - +
103A LYS* 2.7 40.1 + - - -
1174A POP 3.2 8.5 + - - -
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Residues in contact with GLU 102 (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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63A SER* 3.7 26.7 + - - +
68A VAL* 4.5 6.0 - - + +
69A ASP* 4.1 16.3 + - - +
91A VAL* 4.6 2.7 - - + -
92A LEU 3.8 4.0 - - - -
93A ASN* 3.5 19.3 - - - +
100A MET* 5.0 8.5 - - + +
101A ASP* 1.3 87.7 + - - +
103A LYS* 1.3 67.1 + - - +
104A LEU 4.1 0.4 - - - -
163A VAL* 3.8 42.1 - - + +
166A LYS* 5.4 8.0 - - - +
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Residues in contact with LYS 103 (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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54A TYR* 3.0 21.4 + - + -
69A ASP* 3.5 15.7 + - + +
71A LEU* 3.6 18.8 - - + -
91A VAL* 3.8 3.7 - - - +
92A LEU* 2.8 41.9 + - + +
94A MET* 3.8 18.8 - - + -
101A ASP* 2.7 27.0 + - - +
102A GLU* 1.3 77.3 - - - +
104A LEU* 1.3 64.6 - - - +
105A ILE* 3.5 4.2 + - - +
137A PHE* 3.7 37.5 - - + -
140A TYR* 4.9 0.2 - - - -
1174A POP 2.7 26.8 + - - -
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Residues in contact with LEU 104 (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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15A LEU* 5.9 0.4 - - + -
57A VAL* 4.4 10.3 - - + -
68A VAL* 3.9 29.6 - - + -
69A ASP 3.0 17.2 + - - +
70A ALA* 3.7 7.0 - - + -
71A LEU* 2.6 33.6 + - - +
88A LEU* 3.8 21.5 - - + -
90A GLY 3.9 1.8 - - - -
91A VAL* 3.9 17.0 - - + -
103A LYS* 1.3 73.4 - - - +
105A ILE* 1.3 58.1 + - - +
106A ALA 3.9 0.2 - - - -
160A ALA* 3.8 29.8 - - + +
163A VAL* 4.0 12.8 - - + -
164A LEU* 4.3 19.3 - - + -
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LEU* 3.8 22.2 - - + -
73A LEU* 4.0 20.4 - - + -
88A LEU* 3.7 2.9 - - - +
89A VAL* 3.0 40.0 + - + +
90A GLY* 2.9 16.4 + - - +
91A VAL* 3.9 18.6 - - - +
92A LEU* 4.1 6.3 - - + -
103A LYS 3.7 11.4 - - - +
104A LEU* 1.3 73.9 - - - +
106A ALA* 1.3 61.2 + - - +
122A ILE* 4.2 2.5 - - + -
125A LEU* 4.0 17.0 - - + -
130A LEU* 5.9 0.2 - - + -
133A ILE* 5.3 3.8 - - + -
154A PHE* 3.8 29.8 - - + -
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU* 5.3 1.8 - - + -
17A VAL* 5.1 5.4 - - + -
70A ALA* 5.2 3.6 - - + -
71A LEU 2.8 18.2 + - - +
72A VAL* 4.2 5.8 - - + -
73A LEU* 2.9 29.0 + - - +
86A ALA* 4.0 14.4 - - + -
87A ARG 3.2 18.6 - - - +
88A LEU* 4.2 11.4 - - + -
89A VAL* 4.4 2.2 - - - -
104A LEU 3.8 1.1 + - - +
105A ILE* 1.3 75.4 - - - +
107A LEU* 1.3 67.8 + - - +
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Residues in contact with LEU 107 (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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72A VAL* 4.6 0.4 - - - -
73A LEU* 3.0 45.1 - - + +
86A ALA* 3.1 4.0 - - - +
87A ARG* 2.7 64.1 + - - +
89A VAL* 4.1 8.7 - - + -
106A ALA* 1.3 75.8 - - - +
108A PRO* 1.3 73.7 - - + +
116A HIS* 3.7 24.9 - - + +
119A VAL* 3.5 39.0 - - + -
125A LEU* 4.9 5.2 - - + -
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Residues in contact with PRO 108 (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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72A VAL* 3.9 9.0 - - + -
73A LEU 3.1 20.6 - - - +
74A SER* 4.3 5.8 - - - -
78A PHE* 4.5 6.5 - - + -
84A VAL* 3.9 21.1 - - + -
85A LYS 3.5 7.0 - - - +
86A ALA* 3.9 4.4 - - + -
87A ARG* 4.4 5.0 + - - -
107A LEU* 1.3 92.2 - - + +
109A ILE* 1.3 67.5 + - - +
110A ASP* 3.5 2.1 + - - +
112A ILE* 4.3 13.5 - - + -
113A ASP* 3.6 33.4 - - + +
116A HIS* 6.3 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