Contacts of the helix formed by residues 5 - 24 (chain B) in PDB entry 3P9K
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 ALA 5 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B ALA* 1.3 69.1 - - - +
7B ASP* 3.2 7.6 + - - +
8B MET* 3.3 21.5 + - - +
9B ALA* 3.0 23.8 + - - +
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Residues in contact with ALA 6 (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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5B ALA* 1.3 78.1 - - - +
7B ASP* 1.3 66.4 + - - +
9B ALA* 3.5 7.4 + - - +
10B ALA* 3.1 24.6 + - - +
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Residues in contact with ASP 7 (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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5B ALA 3.2 4.4 - - - +
6B ALA* 1.3 78.1 - - - +
8B MET* 1.3 64.4 + - + +
10B ALA* 3.0 8.4 + - - +
11B SER* 2.8 29.1 + - - -
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Residues in contact with MET 8 (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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5B ALA* 3.3 20.5 + - - +
7B ASP* 1.3 77.9 - - + +
9B ALA* 1.3 63.1 + - - +
11B SER* 3.1 18.5 + - - -
12B ALA* 3.1 12.8 + - - +
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Residues in contact with ALA 9 (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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5B ALA 3.0 16.0 + - - +
6B ALA* 3.7 8.3 - - - +
8B MET* 1.3 76.0 - - - +
10B ALA* 1.3 60.6 - - - +
12B ALA* 3.3 20.3 + - - +
13B ASP* 3.4 14.0 + - - +
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Residues in contact with ALA 10 (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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187A LYS* 5.6 8.5 - - - +
350A TYR* 3.8 9.9 + - + +
6B ALA 3.1 17.2 + - - +
7B ASP* 3.0 7.7 + - - +
9B ALA* 1.3 73.3 - - - +
11B SER* 1.3 60.1 + - - +
12B ALA 3.2 1.8 - - - -
13B ASP* 3.5 6.4 + - - +
14B GLU* 3.1 27.4 + - - +
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Residues in contact with SER 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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7B ASP 2.8 12.4 + - - -
8B MET* 3.1 13.9 + - - -
10B ALA* 1.3 76.5 - - - +
12B ALA* 1.3 59.4 + - - +
14B GLU* 3.5 13.0 + - - +
15B ASP* 2.9 43.1 + - - +
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Residues in contact with ALA 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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107A PRO* 6.0 0.2 - - - +
8B MET 3.1 10.7 + - - +
9B ALA* 3.3 13.0 - - - +
10B ALA 3.2 0.2 - - - -
11B SER* 1.3 76.0 - - - +
13B ASP* 1.3 66.7 + - - +
15B ASP* 3.2 12.1 + - - +
16B ALA* 3.2 20.8 + - - +
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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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110A LYS* 3.5 26.2 + - - +
111A PHE* 3.1 29.0 - - + -
350A TYR* 3.4 11.7 - - - +
9B ALA 3.4 12.9 + - - +
10B ALA* 3.9 7.9 - - - +
11B SER 3.4 0.2 - - - -
12B ALA* 1.3 80.0 - - - +
14B GLU* 1.3 62.2 + - - +
16B ALA* 3.3 2.4 + - - -
17B CYS* 3.1 17.7 + - - +
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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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348A TYR* 2.7 38.8 + - - -
350A TYR* 3.1 39.9 + - + -
351A ALA* 2.8 19.8 + - - +
10B ALA 3.1 10.6 + - - +
11B SER* 3.7 13.7 + - - +
12B ALA 3.2 0.2 - - - -
13B ASP* 1.3 75.4 - - - +
15B ASP* 1.3 59.3 + - - +
17B CYS* 3.2 2.3 + - - +
18B MET* 2.9 42.8 + - + +
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Residues in contact with ASP 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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305A PRO* 5.7 0.9 - - - +
11B SER* 2.9 37.9 + - - +
12B ALA* 3.5 10.7 - - - +
14B GLU* 1.3 78.3 - - - +
16B ALA* 1.3 57.2 + - - +
18B MET* 3.1 24.4 + - - +
19B PHE* 2.8 30.8 + - - +
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Residues in contact with ALA 16 (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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107A PRO* 4.1 31.0 - - + +
108A VAL* 3.5 7.4 - - - +
111A PHE* 3.5 23.6 - - + -
12B ALA 3.2 10.9 + - - +
13B ASP* 3.5 4.5 - - - +
14B GLU 3.3 0.2 - - - -
15B ASP* 1.3 78.4 - - - +
17B CYS* 1.3 56.7 - - - +
19B PHE* 3.3 9.2 + - - +
20B ALA* 2.9 27.9 + - - +
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Residues in contact with CYS 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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111A PHE* 3.5 29.3 - - + -
121A MET* 4.0 27.6 - - - -
183A ILE* 4.9 6.1 - - - -
184A ILE* 5.9 0.4 - - - -
350A TYR* 4.4 13.9 - - + -
351A ALA* 4.1 16.6 - - + -
13B ASP 3.1 13.1 + - - +
14B GLU* 3.5 11.4 - - - +
15B ASP 3.1 0.2 - - - -
16B ALA* 1.3 75.9 - - - +
18B MET* 1.3 60.0 + - - +
20B ALA* 3.3 3.2 + - - +
21B LEU* 2.9 31.7 + - - +
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Residues in contact with MET 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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305A PRO* 4.5 18.0 - - + +
306A SER* 4.1 30.3 - - - +
348A TYR* 4.3 5.2 - - - +
351A ALA* 3.8 29.6 - - + -
352A ASN* 4.2 15.0 - - - +
14B GLU* 2.9 28.2 + - + +
15B ASP* 3.1 27.8 + - - +
17B CYS* 1.3 74.5 - - - +
19B PHE* 1.3 61.2 + - - +
21B LEU* 3.2 9.7 + - - +
22B GLN* 2.9 30.1 + - - +
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Residues in contact with PHE 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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84A TYR* 3.4 21.5 - - + -
85A ASN* 3.8 25.8 - - + -
86A VAL* 4.8 0.2 - - + -
108A VAL* 3.7 22.4 - - + -
305A PRO* 4.7 11.3 - - + +
15B ASP 2.8 15.8 + - - +
16B ALA* 3.5 7.4 - - - +
18B MET* 1.3 76.6 - - - +
20B ALA* 1.3 58.5 + - - +
22B GLN* 3.3 22.4 + - - +
23B LEU* 2.9 64.0 + - + +
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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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108A VAL* 3.6 15.0 - - + +
111A PHE* 3.7 32.5 - - + +
112A LEU* 4.2 11.2 - - + +
121A MET* 4.3 6.7 - - + -
16B ALA 2.9 14.5 + - - +
17B CYS* 3.4 9.4 - - - +
19B PHE* 1.3 77.2 - - - +
21B LEU* 1.3 56.3 + - - +
23B LEU* 3.3 5.7 + - - +
24B ALA* 2.9 29.2 + - - +
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Residues in contact with LEU 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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121A MET* 3.5 39.3 - - + -
124A LEU* 4.0 16.4 - - + -
180A HIS* 4.1 13.0 - - + +
263A TRP* 5.7 1.3 - - + -
309A GLY* 6.3 1.8 - - - -
351A ALA* 3.7 38.6 - - + +
352A ASN* 5.5 5.6 - - + +
601A CIY 5.2 3.1 - - - +
17B CYS* 2.9 17.4 + - - +
18B MET* 3.2 10.9 + - + +
20B ALA* 1.3 74.9 - - - +
22B GLN* 1.3 67.6 + - - +
24B ALA* 3.1 15.3 + - + +
25B SER* 3.4 13.2 + - - -
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Residues in contact with GLN 22 (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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305A PRO* 3.5 32.8 - - - +
308A GLN* 3.1 26.9 + - - +
309A GLY* 4.8 7.1 - - - +
312A HIS* 3.5 23.1 + - + +
18B MET 2.9 16.9 + - - +
19B PHE* 3.7 19.9 - - - +
21B LEU* 1.3 75.1 - - - +
23B LEU* 1.3 66.3 + - + +
25B SER* 3.2 6.8 + - - -
26B SER* 3.1 18.9 + - - -
84B TYR* 2.8 25.4 + - - +
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Residues in contact with LEU 23 (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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29A LEU* 4.1 26.7 - - + -
30A PRO* 5.3 0.5 - - - +
33A LEU* 3.8 25.7 - - + +
84A TYR* 5.7 0.9 - - + +
86A VAL* 4.2 20.9 - - + -
108A VAL* 3.9 23.8 - - + -
112A LEU* 4.2 13.5 - - + -
125A ALA* 5.2 0.3 - - - +
129A GLN* 5.0 1.9 + - - +
19B PHE* 2.9 54.7 + - + +
20B ALA* 3.5 4.5 - - - +
22B GLN* 1.3 79.4 - - + +
24B ALA* 1.3 57.8 + - - +
25B SER 2.9 3.6 + - - -
26B SER* 2.8 25.0 + - - +
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Residues in contact with ALA 24 (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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33A LEU* 5.3 0.4 - - - -
112A LEU* 5.3 2.0 - - + +
121A MET* 3.9 13.9 - - + +
124A LEU* 3.4 14.4 - - + +
125A ALA* 3.8 28.5 - - + +
128A ASN* 3.2 15.3 + - - +
129A GLN* 3.2 17.3 + - - -
601A CIY 5.4 1.3 - - - +
20B ALA 2.9 17.2 + - - +
21B LEU* 3.1 10.7 + - - +
23B LEU* 1.3 74.4 - - - +
25B SER* 1.3 57.7 + - - +
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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