Contacts of the strand formed by residues 6 - 16 (chain B) in PDB entry 3BYQ
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 6 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A TYR* 3.8 21.4 - - + +
18A HIS* 3.5 16.0 - - - -
4B ILE* 4.3 10.7 + - + +
5B GLU* 1.3 72.1 - - - +
7B ARG* 1.3 63.4 + - - +
8B LYS 3.6 23.1 - - - +
9B ARG* 3.7 22.4 - - + +
35B ALA* 4.4 3.1 - - + -
36B VAL 3.5 6.7 - - - +
37B ILE* 4.0 14.1 - - + -
59B LEU* 4.0 21.8 - - + -
62B LEU* 4.2 16.4 - - + -
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Residues in contact with ARG 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.8 2.0 - - - +
17A TYR* 2.9 27.3 + - - +
18A HIS* 3.3 48.9 + - + +
19A GLU* 4.5 13.7 - - - +
20A ASN* 4.5 9.2 - - - +
5B GLU 3.7 2.9 + - - +
6B ILE* 1.3 72.4 - - - +
8B LYS* 1.3 79.9 + - + +
36B VAL* 2.8 16.0 + - + +
37B ILE* 5.6 0.9 - - - -
38B ARG 6.1 0.4 - - - +
154B ASP* 2.9 45.1 + - - -
155B ALA* 3.7 11.5 - - - +
157B ARG* 3.5 15.1 - - - +
160B GLU* 2.6 45.4 + - - +
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 2.9 41.8 + - - -
15A THR 3.2 14.4 - - - +
16A THR* 4.1 13.4 + - + +
17A TYR* 4.2 2.5 - - - -
6B ILE* 3.6 2.4 - - - +
7B ARG* 1.3 107.5 - - + +
9B ARG* 1.3 68.8 + - - +
10B THR* 5.0 0.2 - - - -
36B VAL* 2.9 44.4 + - + +
152B ILE* 3.8 15.2 - - + +
154B ASP* 2.9 31.4 + - - +
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Residues in contact with ARG 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL 4.5 0.2 - - - -
14A GLU* 3.4 1.4 - - - +
15A THR* 2.9 39.6 + - - +
17A TYR* 3.5 26.6 + - + -
194A PG4 3.3 20.1 + - - +
6B ILE* 3.7 21.3 - - + +
8B LYS* 1.3 78.6 - - - +
10B THR* 1.3 71.6 + - - +
33B SER* 5.0 0.2 + - - -
34B CYS 3.0 12.8 - - - +
35B ALA* 4.0 5.8 - - + -
62B LEU* 3.6 32.8 + - - +
63B LEU* 4.0 16.1 - - - +
66B GLU* 2.8 41.0 + - - +
152B ILE* 4.8 1.3 - - - -
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Residues in contact with THR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 5.3 1.1 - - - -
13A VAL 3.3 6.7 - - - -
14A GLU* 3.9 22.4 - - + -
195A EDO 4.0 14.4 - - - -
8B LYS* 5.0 0.4 - - - -
9B ARG* 1.3 81.9 - - - +
11B LEU* 1.3 62.4 + - - +
12B ILE* 4.8 11.0 - - - +
32B ALA 3.8 1.0 - - - +
33B SER* 3.4 5.4 + - - -
34B CYS* 2.8 52.4 + - - +
66B GLU* 5.0 1.1 - - - +
151B GLY 4.9 2.0 + - - -
152B ILE* 3.5 28.7 - - + +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU 3.8 0.7 - - - +
12A ILE* 3.4 1.9 - - - +
13A VAL* 2.9 41.5 + - + +
194A PG4 4.1 8.1 - - - -
200A EDO 3.8 29.2 - - - +
10B THR* 1.3 75.3 - - - +
12B ILE* 1.3 67.9 + - - +
13B VAL* 4.3 6.3 - - + -
32B ALA 3.3 12.6 - - - +
33B SER* 4.3 2.2 - - - -
66B GLU* 3.7 33.7 - - + +
67B LEU* 4.1 18.8 - - + -
70B THR* 3.6 30.1 - - + +
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Residues in contact with ILE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 6.0 1.3 - - - -
11A LEU 3.3 4.7 - - - +
12A ILE* 3.5 32.3 - - + -
195A EDO 6.0 0.4 - - - +
10B THR* 4.8 9.4 - - - +
11B LEU* 1.3 81.5 - - - +
13B VAL* 1.3 64.8 + - - +
31B ALA* 3.0 8.2 - - - +
32B ALA* 2.8 54.1 + - + +
34B CYS* 6.2 1.8 - - - -
128B ARG* 5.7 1.3 - - - +
148B ILE* 4.1 10.3 - - + -
149B GLU 3.7 11.0 - - - +
150B ILE* 4.8 6.1 - - + -
151B GLY 5.9 0.2 - - - +
194B EDO 3.2 34.5 - - - +
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ARG 3.9 0.3 - - - +
10A THR* 3.3 4.7 - - - -
11A LEU* 2.9 40.5 + - + +
200A EDO 4.8 4.0 - - - -
11B LEU* 4.7 7.2 - - + -
12B ILE* 1.3 78.3 - - - +
14B GLU* 1.3 61.8 + - - +
15B THR* 4.0 6.1 + - - +
29B LYS* 4.2 19.1 - - + -
30B LEU 3.7 6.3 - - - +
31B ALA* 4.0 5.6 - - + -
70B THR* 3.6 30.3 - - + -
71B LEU* 4.5 4.7 - - + -
200B EDO 3.6 38.9 + - - +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LYS* 2.8 43.3 + - - -
9A ARG 3.4 7.4 - - - +
10A THR* 4.1 9.6 - - + -
12B ILE 4.1 0.6 - - - -
13B VAL* 1.3 72.9 - - - +
15B THR* 1.3 62.7 + - - +
16B THR* 4.0 10.9 + - - +
28B LEU 3.6 1.2 - - - +
29B LYS* 3.3 3.7 - - - -
30B LEU* 2.8 60.4 + - - +
147B SER 4.6 3.1 - - - +
148B ILE* 4.2 16.1 - - + +
149B GLU 5.7 0.3 + - - -
194B EDO 3.6 23.3 + - - -
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Residues in contact with THR 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 3.2 6.6 - - - +
9A ARG* 2.8 39.2 + - - +
13B VAL* 4.0 5.6 + - - +
14B GLU* 1.3 74.1 - - - +
16B THR* 1.3 61.6 + - - +
17B TYR* 3.8 20.6 + - + -
27B PRO* 3.7 28.7 - - + -
28B LEU 3.3 6.5 - - - +
29B LYS* 3.8 12.6 - - + +
204B EDO 2.8 37.4 + - - +
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Residues in contact with THR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 3.9 6.7 - - + +
8A LYS* 4.1 13.6 + - + +
14B GLU* 4.0 20.8 + - - +
15B THR* 1.3 74.3 + - - +
17B TYR* 1.3 62.7 + - - +
18B HIS 3.5 21.5 - - - +
19B GLU* 5.5 1.8 - - + -
27B PRO* 3.2 6.5 - - - +
28B LEU* 2.8 46.7 + - + +
173B VAL* 3.5 26.2 - - + +
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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