Contacts of the strand formed by residues 49 - 60 (chain A) in PDB entry 2BG9
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 ILE 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ASN 4.0 0.2 - - - +
43A VAL* 3.2 3.7 - - - +
44A ASP* 2.9 33.8 + - + +
47A ASN* 3.1 32.8 - - + +
48A GLN* 1.3 75.7 - - - +
50A VAL* 1.3 69.8 + - - +
97A ASP* 4.2 20.0 - - - +
125A LYS* 4.2 28.0 - - + +
126A SER 3.2 9.6 - - - +
127A TYR* 5.0 2.9 - - + -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.8 6.1 - - + -
42A ASN 3.2 4.9 - - - +
43A VAL* 2.9 51.4 - - + -
48A GLN 5.5 1.6 - - - +
49A ILE* 1.3 77.0 - - - +
51A GLU* 1.3 65.9 + - - +
52A THR* 2.9 28.7 - - + -
124A PHE 3.4 0.5 - - - +
125A LYS* 3.5 2.0 - - - -
126A SER* 2.7 50.3 + - - +
128A CYS* 5.5 11.9 - - - -
144A MET* 5.8 2.2 - - + -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 2.1 77.4 + - + +
42A ASN* 2.8 16.1 + - + +
50A VAL* 1.3 73.9 - - - +
52A THR* 1.3 60.4 + - - +
123A ILE* 4.6 8.1 - - + +
124A PHE 3.0 12.1 - - - +
125A LYS* 3.9 31.4 + - + +
97B ASP 5.6 1.6 - - - +
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Residues in contact with THR 52 (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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37A LEU* 3.9 9.9 - - + +
39A GLN 3.8 3.6 - - - -
40A LEU* 3.8 24.9 - - + +
41A ILE 4.6 0.2 - - - +
50A VAL* 2.9 34.3 - - + -
51A GLU* 1.3 72.1 - - - +
53A ASN* 1.3 54.3 + - - +
54A VAL* 3.4 8.5 + - - +
123A ILE* 2.6 39.8 - - - +
124A PHE* 2.9 34.3 + - - -
126A SER* 4.0 6.5 - - - +
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 2.7 29.1 - - - +
38A ILE* 2.9 19.4 + - + +
39A GLN* 2.5 43.5 + - - +
41A ILE* 5.1 3.6 - - - +
52A THR* 1.3 69.7 - - - +
54A VAL* 1.3 63.5 + - - +
122A ALA 3.3 13.5 - - - +
123A ILE* 3.6 22.7 - - - +
149B TYR* 3.8 14.0 + - - -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 4.1 16.8 - - + -
36A GLN 3.8 3.1 - - - -
37A LEU* 3.1 31.2 - - + -
38A ILE* 3.8 2.7 - - - -
52A THR* 3.4 17.3 - - - +
53A ASN* 1.3 70.6 - - - +
55A ARG* 1.3 53.7 + - - +
56A LEU* 4.7 7.2 - - + +
100A PHE* 4.4 19.7 - - + -
122A ALA* 2.3 90.4 + - + +
123A ILE* 4.2 0.9 - - - +
124A PHE* 4.3 11.9 - - + -
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY 3.5 2.3 - - - +
35A LEU* 4.0 0.7 - - - -
36A GLN* 3.3 38.9 + - + +
38A ILE* 2.8 45.5 - - + +
54A VAL* 1.3 74.2 - - - +
56A LEU* 1.3 62.7 + - - +
57A ARG* 3.4 4.4 + - - +
119A THR* 5.2 8.3 - - - +
120A PRO 4.0 5.6 - - - -
121A PRO* 4.4 17.4 - - + +
122A ALA 4.2 0.2 - - - +
93B MET* 5.2 12.5 - - - +
149B TYR* 5.5 5.8 + - - +
201B ASP* 4.2 24.5 + - - +
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Residues in contact with LEU 56 (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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33A VAL* 3.6 21.3 - - + -
34A GLY 3.7 7.0 - - - +
35A LEU* 5.1 6.3 - - + +
54A VAL* 3.7 8.5 - - + -
55A ARG* 1.3 70.8 - - - +
57A ARG* 1.3 95.9 + - - +
58A GLN* 3.3 18.6 - - + +
90A LEU* 3.0 43.1 - - + -
100A PHE* 4.1 14.1 - - + -
103A VAL* 6.1 2.7 - - + -
118A TRP 2.9 6.1 - - - +
119A THR* 2.7 32.4 - - - -
120A PRO* 3.4 17.0 + - + +
122A ALA* 5.6 1.8 - - + -
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Residues in contact with ARG 57 (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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32A THR* 3.5 5.5 - - + +
33A VAL 4.2 0.7 - - - -
34A GLY* 2.8 42.2 + - - +
35A LEU 5.7 0.4 - - - -
36A GLN* 5.9 6.0 - - - +
55A ARG 3.4 2.3 + - - +
56A LEU* 1.3 86.2 - - - +
58A GLN* 1.3 58.4 + - - +
59A GLN* 4.7 5.8 - - + +
117A MET* 4.5 9.9 - - + +
119A THR* 3.1 18.6 - - + -
161A GLU* 2.4 53.3 + - + +
162A SER* 3.7 6.9 + - - -
164A ARG* 6.0 1.6 - - - +
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 5.5 0.9 - - + -
32A THR 3.5 5.6 - - - +
33A VAL* 5.4 0.4 - - + -
56A LEU* 3.3 28.6 - - + +
57A ARG* 1.3 72.3 - - - +
59A GLN* 1.3 67.6 + - - +
60A TRP* 3.2 18.9 - - + -
88A PRO* 3.3 18.0 + - + +
90A LEU* 3.1 37.9 - - + +
103A VAL* 5.9 1.2 - - - +
116A ILE 3.9 0.3 - - - +
117A MET* 3.4 1.7 - - - -
118A TRP* 2.8 79.3 + - - +
119A THR* 3.9 0.6 - - - +
120A PRO* 4.2 5.7 - - - +
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Residues in contact with GLN 59 (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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30A ASP* 3.8 1.2 - - - +
31A ILE* 3.0 7.6 - - - -
32A THR* 3.0 44.7 + - + +
57A ARG* 4.7 7.3 - - + +
58A GLN* 1.3 81.6 + - - +
60A TRP* 1.3 67.8 + - - +
115A LYS* 3.8 21.9 - - + +
116A ILE 2.9 22.2 - - - +
117A MET* 2.5 54.1 - - - +
161A GLU* 5.7 3.6 - - - +
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Residues in contact with TRP 60 (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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21A PRO* 5.7 5.6 - - + -
29A VAL* 5.2 3.1 - - + -
30A ASP* 3.5 10.1 - - - +
31A ILE* 3.0 52.0 - - + -
58A GLN* 3.2 20.6 - - + -
59A GLN* 1.3 78.2 - - - +
61A ILE* 1.3 69.8 + - - +
62A ASP* 5.5 1.1 - - + -
85A VAL* 3.6 27.8 - - + +
86A TRP* 4.5 7.0 - + - -
88A PRO* 3.7 22.7 - - + -
108A LEU* 3.8 16.4 - - + +
115A LYS* 4.9 1.1 - - - +
116A ILE* 3.1 62.1 + - + +
118A TRP* 3.4 35.7 - + + -
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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