Contacts of the strand formed by residues 29 - 44 (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 VAL 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ARG* 4.9 11.2 - - + -
21A PRO* 4.1 37.7 - - + +
22A VAL* 5.1 6.7 - - + -
27A HIS* 4.4 2.9 - - - -
28A PHE* 1.3 72.4 - - - +
30A ASP* 1.3 64.1 + - - +
31A ILE* 3.2 25.9 + - + -
60A TRP* 5.2 2.5 - - + -
61A ILE 4.7 7.9 - - - +
86A TRP* 3.4 26.5 - - + -
155A LYS 3.2 18.0 + - - +
156A VAL* 3.3 16.6 - - + +
157A SER* 3.5 6.4 + - - -
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Residues in contact with ASP 30 (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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27A HIS* 4.2 21.4 + - + +
28A PHE 3.3 5.6 + - - -
29A VAL* 1.3 70.5 - - - +
31A ILE* 1.3 67.8 + - - +
32A THR* 4.4 8.1 + - - -
59A GLN 4.9 1.2 - - - +
60A TRP* 3.5 16.3 - - - +
61A ILE* 4.3 13.3 + - + +
157A SER* 4.4 9.0 + - - +
159A SER* 4.4 12.1 + - - -
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Residues in contact with ILE 31 (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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29A VAL* 3.2 47.4 + - + +
30A ASP* 1.3 73.3 - - - +
32A THR* 1.3 67.4 + - - +
33A VAL* 5.9 0.2 - - + -
58A GLN* 5.5 0.9 - - + -
59A GLN 3.0 3.4 - - - +
60A TRP* 3.0 51.6 - - + -
86A TRP* 3.3 22.2 - - + -
88A PRO* 4.3 18.2 - - + -
90A LEU* 6.2 0.4 - - + -
156A VAL* 3.7 9.0 - - + -
157A SER 2.8 26.3 + - - +
158A ILE* 3.2 12.5 - - + -
159A SER* 3.0 12.3 + - - -
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Residues in contact with THR 32 (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* 4.4 9.4 + - - -
31A ILE* 1.3 76.6 - - - +
33A VAL* 1.3 70.3 + - - +
57A ARG* 3.5 5.6 - - - +
58A GLN* 3.5 3.5 - - - +
59A GLN* 3.0 41.7 + - + +
159A SER* 2.4 35.3 + - - +
160A PRO 2.7 30.0 + - - +
161A GLU* 3.8 8.7 - - + -
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Residues in contact with VAL 33 (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* 1.3 77.8 - - - +
34A GLY* 1.3 64.1 + - - +
35A LEU* 4.9 4.5 - - + +
56A LEU* 3.6 27.1 - - + -
57A ARG* 3.6 4.0 - - - -
58A GLN* 5.5 0.4 - - - -
90A LEU* 4.5 6.5 - - + -
146A LEU* 5.8 9.9 - - + +
147A GLY* 5.6 0.4 - - - -
158A ILE* 2.9 47.3 - - + -
159A SER 2.7 14.1 + - - +
160A PRO* 3.5 1.2 - - - +
161A GLU* 3.2 25.3 + - - +
201A ILE* 4.3 19.7 - - + +
203A TYR* 5.8 1.3 - - - +
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Residues in contact with GLY 34 (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* 1.3 79.5 - - - +
35A LEU* 1.3 60.3 + - - +
36A GLN* 3.9 0.3 + - - +
55A ARG 3.5 3.1 - - - +
56A LEU* 4.1 1.8 - - - -
57A ARG* 2.8 63.1 + - - +
161A GLU* 3.6 7.6 - - - -
201A ILE* 5.2 2.9 - - - -
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Residues in contact with LEU 35 (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* 4.9 3.7 - - + +
34A GLY* 1.3 73.3 - - - +
36A GLN* 1.3 57.7 + - - +
37A LEU* 3.0 48.9 - - + +
54A VAL* 4.1 15.7 - - + -
55A ARG 4.0 3.8 - - - -
56A LEU* 5.1 7.0 - - + +
57A ARG* 6.3 0.2 - - - -
92A LEU* 5.5 3.1 - - + -
124A PHE* 5.6 3.6 - - + -
146A LEU* 4.3 6.5 - - + -
164A ARG* 2.5 48.2 + - - +
201A ILE* 5.3 4.0 - - + +
203A TYR* 2.5 45.5 - - + +
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Residues in contact with GLN 36 (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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34A GLY 3.9 1.3 + - - +
35A LEU* 1.3 76.6 - - - +
37A LEU* 1.3 83.8 + - - +
38A ILE* 2.9 41.4 + - - +
55A ARG* 3.3 30.0 + - + +
57A ARG* 5.9 6.3 - - - +
164A ARG* 2.9 10.5 - - - +
168A SER* 6.2 0.2 - - - +
169A THR* 4.7 6.2 - - + +
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Residues in contact with LEU 37 (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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35A LEU* 3.0 36.1 - - + +
36A GLN* 1.3 83.3 + - - +
38A ILE* 1.3 51.3 + - - +
39A GLN 3.2 0.2 - - - -
40A LEU* 3.7 24.7 - - + -
52A THR* 3.9 11.4 - - + +
53A ASN 2.7 12.8 - - - +
54A VAL* 3.1 30.1 - - + -
124A PHE* 5.7 0.7 - - + -
164A ARG* 2.9 16.0 + - - +
166A ASP* 3.8 20.6 - - - +
169A THR* 2.4 40.6 + - - +
181A TYR* 5.6 3.6 - - + +
203A TYR* 5.6 1.8 - - + -
205A PHE* 4.7 15.5 - - + -
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Residues in contact with ILE 38 (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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36A GLN* 2.7 34.5 + - - +
37A LEU* 1.3 73.0 - - - +
39A GLN* 1.3 89.9 + - + +
53A ASN* 2.9 25.1 + - + +
54A VAL 3.8 4.7 - - - -
55A ARG* 2.8 65.3 - - + +
122A ALA 4.9 0.2 - - - +
169A THR* 3.1 14.2 - - - +
149B TYR* 5.8 1.6 - - - +
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Residues in contact with GLN 39 (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 3.2 1.2 - - - -
38A ILE* 1.3 112.5 + - + +
40A LEU* 1.3 65.2 + - - +
41A ILE* 5.2 0.3 - - - +
53A ASN* 2.5 51.7 + - - +
169A THR* 3.7 17.7 - - - +
171A MET* 6.5 0.2 - - - -
93B MET 5.7 1.0 - - - +
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Residues in contact with LEU 40 (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* 3.7 31.0 - - + -
39A GLN* 1.3 88.8 - - - +
41A ILE* 1.3 63.0 + - - +
43A VAL* 5.2 0.7 - - + -
50A VAL* 4.8 7.9 - - + -
51A GLU 3.9 7.2 - - - +
52A THR* 3.8 17.3 - - + -
166A ASP* 4.7 9.2 - - - +
169A THR* 3.8 12.9 + - - +
170A PHE* 4.5 15.0 - - + -
171A MET* 3.8 46.2 - - + +
176A TRP* 5.1 9.9 - - + +
205A PHE* 6.0 2.9 - - + -
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Residues in contact with ILE 41 (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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40A LEU* 1.3 75.1 - - - +
42A ASN* 1.3 101.8 + - + +
51A GLU* 2.1 75.7 + - + +
53A ASN* 5.1 5.2 - - - +
123A ILE* 3.4 30.3 - - + -
171A MET* 3.8 10.7 - - - +
97B ASP* 4.7 17.0 - - - +
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Residues in contact with ASN 42 (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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40A LEU 3.8 0.8 - - - -
41A ILE* 1.3 119.3 + - + +
43A VAL* 1.3 67.5 + - - +
49A ILE 4.0 0.3 - - - +
50A VAL* 3.2 3.3 - - - -
51A GLU* 2.8 33.2 + - + +
171A MET* 4.0 12.1 - - - +
47B ASN* 5.5 7.5 - - - +
49B GLU* 4.5 14.1 + - - -
97B ASP* 5.9 0.6 + - - -
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Residues in contact with VAL 43 (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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40A LEU* 5.2 4.5 - - + -
42A ASN* 1.3 81.1 - - - +
44A ASP* 1.3 80.5 + - - +
45A GLU* 4.0 5.6 - - - +
48A GLN* 5.5 1.1 - - - -
49A ILE 3.2 7.2 - - - +
50A VAL* 2.9 42.8 - - + -
171A MET* 4.4 3.3 - - + +
176A TRP* 3.4 43.7 - - + -
209A ARG* 4.6 12.4 + - - +
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Residues in contact with ASP 44 (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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43A VAL* 1.3 76.3 - - - +
45A GLU* 1.3 55.0 + - - +
46A VAL* 3.1 5.1 - - - +
47A ASN* 2.9 37.4 + - + +
48A GLN* 2.5 36.7 + - - -
49A ILE* 2.9 16.8 + - + +
209A ARG* 5.2 0.7 - - - +
270A ALA 3.9 16.6 - - - +
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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