Contacts of the helix formed by residues 2 - 20 (chain B) in PDB entry 4BPK
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 SER 2 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A ALA* 5.0 0.3 - - - +
175A ASN* 3.1 42.9 + - - +
1201A CD 4.1 15.2 - - - -
3B GLN* 1.3 62.0 + - - +
4B SER* 3.7 6.3 - - - +
5B ASN* 3.2 22.3 - - - +
6B ARG* 2.9 29.1 + - - +
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Residues in contact with GLN 3 (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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2B SER* 1.3 78.9 + - - +
4B SER* 1.3 57.5 + - - +
6B ARG* 3.5 12.6 + - - +
7B GLU* 2.9 60.0 + - - +
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Residues in contact with SER 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A MET* 3.1 25.5 - - - +
188A TRP* 6.1 0.5 - - - -
2B SER 3.2 5.3 - - - +
3B GLN* 1.3 80.7 - - - +
5B ASN* 1.3 65.8 + - - +
7B GLU* 3.3 15.7 + - - +
8B LEU* 3.1 19.2 + - - +
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Residues in contact with ASN 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA* 4.5 2.9 - - - +
174A LEU* 3.9 32.1 + - + +
175A ASN* 2.1 47.3 + - - +
179A GLU* 2.8 24.5 + - - +
188A TRP* 4.4 12.3 + - - -
2B SER 3.2 9.2 - - - +
4B SER* 1.3 77.0 + - - +
6B ARG* 1.3 66.4 - - - +
8B LEU* 3.2 8.4 + - - +
9B VAL* 3.0 27.4 + - - +
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Residues in contact with ARG 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A SER* 5.7 4.6 + - - -
167A ALA* 5.5 7.4 - - + +
168A ALA* 6.0 3.8 - - - +
171A ALA* 3.9 20.1 - - + +
2B SER 2.9 19.1 + - - +
3B GLN* 3.9 14.4 - - - +
4B SER 3.3 0.2 - - - -
5B ASN* 1.3 76.3 - - - +
7B GLU* 1.3 58.5 + - - +
9B VAL* 3.2 3.0 + - + +
10B VAL* 2.9 47.4 + - + +
24B TRP* 3.7 25.9 - - - +
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A MET* 3.7 14.7 - - + +
87A LYS* 3.9 17.8 - - - +
3B GLN* 2.9 54.0 + - - +
4B SER* 3.4 15.3 - - - +
5B ASN 3.2 0.2 - - - -
6B ARG* 1.3 77.9 - - - +
8B LEU* 1.3 55.7 + - - +
10B VAL* 3.5 5.0 + - - +
11B ASP* 3.0 29.6 + - - +
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Residues in contact with LEU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A MET* 4.9 6.7 - - + -
86A VAL* 3.9 20.0 - - + -
87A LYS* 3.8 29.4 - - + +
90A LEU* 3.7 20.6 - - + -
144A PHE* 4.0 10.3 - - + -
174A LEU* 4.9 3.1 - - + -
188A TRP* 3.5 45.1 - - + +
4B SER 3.1 11.9 + - - +
5B ASN* 3.2 11.9 + - - +
7B GLU* 1.3 73.4 - - - +
9B VAL* 1.3 66.2 + - - +
11B ASP* 3.4 3.6 + - - +
12B PHE* 3.1 22.3 + - - +
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 4.0 14.6 - - + -
167A ALA* 3.6 25.6 - - + +
170A MET* 3.8 17.5 - - + -
171A ALA* 3.9 15.7 - - - +
174A LEU* 3.6 24.0 - - + -
5B ASN 3.0 16.9 + - - +
6B ARG* 3.6 8.5 - - + +
8B LEU* 1.3 75.7 - - - +
10B VAL* 1.3 58.5 + - + +
12B PHE* 3.2 3.1 + - - +
13B LEU* 2.9 53.8 + - + +
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ALA* 4.8 5.6 - - + -
6B ARG* 2.9 47.9 + - + +
7B GLU* 4.0 4.7 - - - +
9B VAL* 1.3 74.6 - - + +
11B ASP* 1.3 59.6 + - - +
13B LEU* 4.1 5.3 - - - +
14B SER* 2.7 36.8 + - - +
24B TRP* 3.5 53.8 - - + +
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Residues in contact with ASP 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 5.5 0.9 - - - +
87A LYS* 3.5 40.4 + - + +
91A ARG* 2.8 51.4 + - - +
1202A EDO 2.6 23.8 + - - -
7B GLU 3.0 17.8 + - - +
8B LEU* 3.7 5.1 - - - +
9B VAL 3.3 0.2 - - - -
10B VAL* 1.3 79.2 - - - +
12B PHE* 1.3 62.8 + - - +
14B SER* 3.4 3.3 + - - -
15B TYR* 3.2 10.4 + - - +
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Residues in contact with PHE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.4 45.1 - - + -
91A ARG* 4.2 11.2 - - + -
94A GLY* 4.2 7.9 - - - -
141A VAL* 5.2 0.7 - - + -
144A PHE* 3.2 55.2 - + + -
145A SER* 3.8 16.4 - - - -
8B LEU 3.1 16.8 + - - +
9B VAL 3.7 3.6 - - - +
11B ASP* 1.3 81.3 + - - +
13B LEU* 1.3 70.8 + - + +
15B TYR* 3.3 7.2 + - - +
16B LYS* 3.0 56.4 + - + +
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLY 3.8 7.2 - - - -
148A GLY* 3.6 33.4 - - - +
151A CYS* 3.8 19.5 - - + -
167A ALA* 3.6 36.1 - - + -
170A MET* 3.9 13.7 - - + -
9B VAL* 2.9 28.6 + - + +
10B VAL 4.1 2.2 - - - +
12B PHE* 1.3 76.4 - - + +
14B SER* 1.3 60.1 + - - +
16B LYS* 3.3 3.4 + - - +
17B LEU* 2.9 42.1 + - + +
24B TRP* 4.3 15.5 - - + -
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Residues in contact with SER 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 4.6 5.6 - - - -
10B VAL* 2.7 26.1 + - - +
11B ASP* 3.6 7.0 - - - -
12B PHE 3.3 0.2 - - - -
13B LEU* 1.3 75.9 - - - +
15B TYR* 1.3 57.5 + - - +
17B LEU* 3.8 2.2 - - - +
18B SER* 2.9 32.1 + - - -
23B SER* 5.5 0.2 - - - -
24B TRP* 3.3 36.9 + - - +
84B ALA* 4.1 13.9 - - - +
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Residues in contact with TYR 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 5.7 3.6 + - - -
91A ARG* 3.3 73.9 - - + +
92A GLU* 5.8 1.4 - - - +
95A ASP* 2.6 30.9 + - - -
11B ASP 3.2 4.2 + - - +
12B PHE* 3.3 9.0 - + - +
14B SER* 1.3 76.6 - - - +
16B LYS* 1.3 79.4 + - - +
18B SER* 2.8 26.4 + - - -
19B GLN* 2.9 37.8 + - + +
88B GLN* 5.6 3.1 - - - -
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Residues in contact with LYS 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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95A ASP* 3.1 22.3 + - - +
98A GLU* 2.8 40.6 + - - +
148A GLY* 4.2 26.0 - - - +
149A ALA 5.8 0.2 - - - +
152A VAL* 4.2 4.8 - - + +
12B PHE* 3.0 45.9 + - + +
13B LEU 3.7 3.8 - - - +
15B TYR* 1.3 92.8 - - - +
17B LEU* 1.3 63.7 + - + +
19B GLN* 2.8 41.8 + - - +
20B LYS* 3.4 13.9 + - - +
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Residues in contact with LEU 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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151A CYS* 4.2 8.3 - - + -
152A VAL* 4.1 26.7 - - + +
155A VAL* 3.9 27.8 - - + -
163A VAL* 3.9 22.9 - - + -
13B LEU* 2.9 26.3 + - + +
14B SER 3.8 2.7 - - - +
16B LYS* 1.3 77.6 - - + +
18B SER* 1.3 56.6 + - - +
20B LYS* 3.1 8.0 + - - -
22B TYR* 2.7 48.6 + - + +
23B SER 4.2 3.8 - - - +
24B TRP* 3.9 29.8 - - + +
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B SER 2.9 17.4 + - - -
15B TYR* 2.8 21.1 + - - -
17B LEU* 1.3 76.0 - - - +
19B GLN* 1.3 64.9 + - - +
21B GLY* 3.1 13.9 + - - -
22B TYR 3.2 13.8 + - - -
23B SER* 5.7 1.1 - - - -
88B GLN* 4.4 31.5 + - - -
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Residues in contact with GLN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASP* 3.0 24.9 + - - -
98A GLU* 4.7 0.3 - - - +
15B TYR* 2.9 37.3 + - + +
16B LYS* 2.8 39.7 + - - +
17B LEU 3.2 0.2 - - - -
18B SER* 1.3 82.7 + - - +
20B LYS* 1.3 65.4 + - + +
21B GLY 3.3 0.6 + - - -
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Residues in contact with LYS 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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105A PHE* 6.6 0.4 - - - -
152A VAL* 3.8 28.0 - - + -
16B LYS 3.4 13.0 + - - +
17B LEU 3.1 8.9 + - - +
19B GLN* 1.3 82.3 - - - +
21B GLY* 1.3 63.0 + - - +
22B TYR* 3.3 30.8 + - + -
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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
------------------------------------------------------------
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