Contacts of the strand formed by residues 11 - 22 (chain B) in PDB entry 3N6J
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 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B VAL* 1.3 71.7 - - - +
12B THR* 1.3 60.4 + - - +
13B ASP 3.9 15.9 - - - +
44B LEU* 4.3 10.5 - - + -
45B THR 3.5 8.7 - - - +
46B ASP* 3.9 0.9 - - - +
73B VAL* 3.9 19.3 - - + +
74B VAL* 3.7 21.8 - - + -
75B GLY* 2.8 30.8 + - - -
76B ARG 3.2 19.9 + - - +
77B PRO 4.9 0.2 - - - -
78B ILE* 3.1 35.2 - - + -
84B ILE* 5.2 1.6 - - + -
121B LEU* 3.7 24.0 - - + -
124B LEU* 3.7 18.6 - - + -
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Residues in contact with THR 12 (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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10B VAL* 3.3 17.7 + - + +
11B ILE* 1.3 74.8 - - - +
13B ASP* 1.3 61.4 + - - +
45B THR* 2.6 28.4 + - - -
46B ASP 3.6 5.5 + - - -
47B ASN* 3.6 23.3 - - + -
74B VAL* 3.7 18.9 - - - +
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Residues in contact with ASP 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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11B ILE* 3.7 2.9 - - - +
12B THR* 1.3 83.7 - - - +
14B MSE 1.3 65.6 + - - +
15B LYS* 3.4 36.3 + - - +
43B ILE 3.6 0.6 - - - +
44B LEU* 3.3 4.7 - - - +
45B THR* 2.8 48.9 + - - +
74B VAL* 4.0 5.8 - - - +
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Residues in contact with MSE 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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13B ASP* 1.3 78.4 + - - +
15B LYS* 1.3 68.4 + - - +
16B VAL* 4.2 4.3 - - + -
42B VAL* 4.2 11.9 - - + -
43B ILE 3.1 4.5 - - - -
44B LEU* 3.4 17.7 - - + -
66B LEU* 3.6 43.7 - - + +
69B ALA* 4.7 3.8 - - + -
70B ILE* 3.7 55.2 - - + +
73B VAL* 3.9 21.5 - - + -
74B VAL* 3.9 9.6 - - + +
117B LEU* 3.8 20.4 - - + -
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Residues in contact with LYS 15 (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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13B ASP* 3.4 25.7 + - - +
14B MSE 1.3 74.3 - - - +
16B VAL* 1.3 64.4 + - - +
17B ILE* 4.0 27.1 - - + -
41B ILE 3.3 1.0 - - - +
42B VAL* 3.1 9.5 - - - +
43B ILE* 2.6 56.1 + - + +
45B THR* 6.6 0.2 - - - -
405B MSE 4.0 19.7 - - + -
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B MSE 4.2 11.0 - - + -
15B LYS* 1.3 78.9 - - - +
17B ILE* 1.3 63.9 + - - +
18B PRO* 3.7 5.9 - - - +
40B ASN* 5.1 3.4 - - + +
41B ILE 3.3 4.7 - - - +
42B VAL* 4.8 1.1 - - + -
63B GLU* 3.6 42.7 - - + +
66B LEU* 3.5 43.7 - - + +
67B THR* 3.9 10.8 - - - +
70B ILE* 4.7 8.7 - - + +
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Residues in contact with ILE 17 (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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15B LYS* 4.0 12.3 - - + -
16B VAL* 1.3 81.9 - - - +
18B PRO* 1.3 64.2 - - + +
19B VAL* 3.7 0.4 + - + -
40B ASN* 4.5 1.8 - - - -
41B ILE* 2.8 46.5 + - - +
43B ILE* 3.4 26.9 - - + -
405B MSE 3.9 24.9 - - + -
408B VAL* 4.1 21.1 - - + +
409B LEU* 4.7 7.2 - - + -
412B HIS* 3.6 37.2 - - + +
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Residues in contact with PRO 18 (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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16B VAL 3.7 8.5 - - - +
17B ILE* 1.3 85.3 - - - +
19B VAL* 1.3 59.8 + - - +
39B ARG 3.5 7.6 - - - +
40B ASN* 3.6 8.1 - - - +
63B GLU* 3.2 39.3 - - + +
412B HIS* 2.9 47.3 + - + +
415B HIS* 3.4 34.8 - - + +
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Residues in contact with VAL 19 (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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17B ILE* 3.9 3.4 - - + +
18B PRO* 1.3 80.1 - - - +
20B ALA* 1.3 60.0 + - - +
38B THR* 3.3 4.3 - - - -
39B ARG* 2.9 40.0 + - + +
41B ILE* 3.8 28.5 - - + -
345B PHE* 3.4 27.6 - - + -
379B LEU* 4.8 2.0 - - + -
408B VAL* 3.8 30.5 - - + +
411B ALA* 3.5 19.5 - - + -
412B HIS 4.0 0.2 - - - +
415B HIS* 3.4 7.6 + - - -
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Residues in contact with ALA 20 (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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19B VAL* 1.3 75.0 - - - +
21B GLY* 1.3 58.3 + - - +
36B TYR* 4.7 4.0 - - + -
37B PHE 3.3 9.4 - - - +
38B THR* 4.4 0.9 - - + -
345B PHE* 3.3 16.3 - - - -
377B PHE* 5.5 0.7 - - - -
411B ALA* 3.0 19.2 + - - +
414B LEU* 3.8 19.5 - - + +
415B HIS* 3.6 27.6 - - + +
418B LEU* 4.0 18.6 - - + -
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Residues in contact with GLY 21 (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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20B ALA* 1.3 76.8 - - - +
22B HIS* 1.3 68.7 + - - -
36B TYR* 3.2 12.0 - - - -
37B PHE* 2.7 49.4 + - - -
345B PHE* 3.8 9.0 - - - -
377B PHE* 6.3 1.6 - - - -
414B LEU* 4.7 2.7 - - - +
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Residues in contact with HIS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY* 1.3 73.9 - - - -
23B ASP* 1.3 52.3 + - - +
35B PRO 3.5 3.4 - - - -
36B TYR* 3.4 27.2 + + - -
37B PHE* 3.7 3.1 - - - -
164B PRO 4.9 3.1 - - - -
166B GLN* 3.7 42.0 + - + +
180B ARG* 3.9 9.3 + - - -
373B GLN* 2.8 28.3 + - - +
376B ASP* 3.5 24.3 + - - +
377B PHE* 6.0 3.6 - - - +
414B LEU* 3.7 27.4 - - + +
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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