Contacts of the helix formed by residues 5 - 21 (chain B) in PDB entry 1A74
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 ASN 5 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU 4.1 0.6 + - - -
4B THR* 1.3 74.7 - - - +
6B ALA* 1.3 57.8 + - - +
8B ILE* 3.3 7.0 + - - +
9B LEU* 3.0 42.3 + - - +
84B LEU* 4.0 31.5 - - - +
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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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4B THR* 3.2 7.4 + - - +
5B ASN* 1.3 78.6 - - - +
7B GLN* 1.3 60.0 + - + +
9B LEU* 3.6 10.6 + - - +
10B ALA* 3.2 26.2 + - - +
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Residues in contact with GLN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ALA* 3.5 25.9 - - + +
3B LEU* 3.7 3.8 + - - +
4B THR* 3.0 43.2 + - + +
6B ALA* 1.3 75.8 - - + +
8B ILE* 1.3 64.8 + - - +
10B ALA* 3.6 7.1 + - - +
11B VAL* 3.1 27.8 + - - +
68B ILE* 3.2 28.4 - - + +
69B ASN* 3.5 15.1 + - - +
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Residues in contact with ILE 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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2B ALA 3.2 36.1 - - - +
3B LEU 4.8 3.4 - - - +
4B THR 2.9 21.7 + - - +
5B ASN* 3.7 5.4 - - - +
7B GLN* 1.3 75.4 - - - +
9B LEU* 1.3 65.7 + - - +
11B VAL* 3.0 14.3 + - + +
12B ILE* 3.0 18.7 + - + +
75B TRP* 5.1 3.4 - - + +
83B LEU* 3.6 39.3 - - + +
84B LEU* 3.3 31.4 - - + -
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Residues in contact with LEU 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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157A ARG* 3.4 47.7 - - - +
5B ASN* 3.0 29.3 + - - +
6B ALA* 3.8 8.7 - - - +
7B GLN 3.4 0.2 - - - -
8B ILE* 1.3 76.0 - - - +
10B ALA* 1.3 58.5 + - - +
12B ILE* 3.0 8.8 + - + +
13B ASP* 2.8 35.7 + - - +
84B LEU* 3.5 28.9 - - + -
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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
----------------------------------------------------------
6B ALA 3.2 15.8 + - - +
7B GLN* 3.7 9.2 - - - +
9B LEU* 1.3 78.7 - - - +
11B VAL* 1.3 58.4 + - + +
13B ASP* 3.7 8.4 - - - +
14B SER* 3.0 29.8 + - - -
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ALA 4.3 7.4 - - - +
7B GLN 3.1 17.7 + - - +
8B ILE* 3.0 12.1 + - + +
10B ALA* 1.3 74.7 - - + +
12B ILE* 1.3 61.7 + - - +
14B SER* 3.3 6.9 + - - -
15B TRP* 3.0 27.9 + - - +
64B TYR* 4.0 12.6 - - + -
66B ARG* 4.6 6.1 - - + -
68B ILE* 4.4 12.3 - - + -
75B TRP* 3.7 40.8 - - + -
80B VAL* 4.0 13.5 - - + -
83B LEU* 4.1 7.9 - - + -
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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
----------------------------------------------------------
157A ARG* 3.6 28.7 - - + -
8B ILE* 3.0 32.0 + - + +
9B LEU* 3.5 20.0 - - + +
11B VAL* 1.3 76.2 - - - +
13B ASP* 1.3 57.5 + - - +
15B TRP* 3.6 2.1 - - + +
16B GLU* 3.0 40.4 + - + +
80B VAL* 3.4 33.2 - - + +
81B PRO* 4.0 22.0 - - + +
83B LEU* 4.5 5.4 - - + +
84B LEU* 4.6 8.7 - - + +
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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
----------------------------------------------------------
157A ARG* 2.9 48.0 + - - +
158A GLY 5.4 0.2 + - - -
160A HIS* 4.9 3.5 - - - -
9B LEU* 2.8 16.9 + - - +
10B ALA* 3.7 9.1 - - - +
11B VAL 3.2 0.2 - - - -
12B ILE* 1.3 75.8 - - - +
14B SER* 1.3 64.0 + - - +
16B GLU* 3.5 6.2 + - - +
17B GLU* 3.1 23.6 + - - +
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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
----------------------------------------------------------
10B ALA 3.0 20.0 + - - -
11B VAL* 3.3 7.6 + - - -
13B ASP* 1.3 73.7 - - - +
15B TRP* 1.3 58.9 + - - +
17B GLU* 3.4 8.4 + - - +
18B THR* 2.7 38.1 + - - +
64B TYR* 3.2 16.7 + - - -
66B ARG* 4.2 15.6 - - - -
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Residues in contact with TRP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL 3.0 20.1 + - - +
12B ILE 3.6 3.6 - - - +
14B SER* 1.3 76.5 + - - +
16B GLU* 1.3 92.8 + - + +
18B THR* 3.5 1.3 + - - +
19B VAL* 3.0 41.7 + - + +
54B PHE* 3.6 23.7 - + - -
64B TYR* 3.6 20.0 - + + -
77B SER 2.9 28.8 + - - -
78B HIS* 4.7 2.5 - - - -
80B VAL* 3.4 34.6 - - + +
81B PRO* 3.2 36.3 - - + -
106B HIS* 3.1 32.8 - + + -
108B PRO* 4.0 19.5 - - + -
111B LEU* 4.5 2.0 - - + -
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Residues in contact with GLU 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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155A GLN 4.6 1.6 - - - +
156A GLN* 3.5 12.1 - - - +
157A ARG* 2.8 34.8 + - - +
158A GLY* 3.2 23.7 + - - -
160A HIS* 4.1 14.4 + - + +
161A PHE* 3.3 25.0 - - + -
12B ILE* 3.0 28.4 + - + +
13B ASP* 3.8 6.9 - - - +
15B TRP* 1.3 93.6 - - + +
17B GLU* 1.3 54.2 + - - +
20B GLY* 2.6 34.5 + - - -
81B PRO* 5.9 1.6 - - - +
108B PRO* 4.8 1.8 - - + +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A HIS* 3.8 30.2 + - + -
13B ASP 3.1 18.4 + - - +
14B SER* 3.5 8.7 - - - +
15B TRP 3.2 0.2 - - - -
16B GLU* 1.3 78.6 - - - +
18B THR* 1.3 65.8 + - + +
20B GLY* 3.3 7.6 + - - -
21B GLN* 3.5 22.2 + - + +
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Residues in contact with THR 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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14B SER* 2.7 23.1 + - - +
15B TRP* 4.0 5.4 - - - +
17B GLU* 1.3 77.0 - - + +
19B VAL* 1.3 62.0 + - - +
21B GLN* 2.9 27.9 + - - +
22B PHE* 3.5 13.2 + - - -
51B GLY* 4.6 1.2 - - - -
52B VAL* 4.0 33.2 + - + +
54B PHE* 3.3 23.0 - - + -
64B TYR* 4.5 3.4 - - - +
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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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161A PHE* 3.6 16.6 - - + -
15B TRP* 3.0 39.0 + - + +
16B GLU* 3.9 2.2 - - - +
18B THR* 1.3 72.5 + - - +
20B GLY* 1.3 57.6 + - - +
21B GLN 2.8 10.7 + - - -
22B PHE* 2.8 36.0 + - + +
42B TYR* 3.6 8.8 - - + -
54B PHE* 3.4 28.7 - - + -
106B HIS* 3.6 36.1 - - + +
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Residues in contact with GLY 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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160A HIS* 4.1 15.2 - - - +
161A PHE* 3.5 17.0 - - - -
16B GLU 2.6 24.2 + - - -
17B GLU 3.7 4.0 - - - -
18B THR 3.1 0.6 - - - -
19B VAL* 1.3 71.2 - - - +
21B GLN* 1.3 70.5 + - - +
22B PHE 3.5 1.0 - - - +
24B VAL* 5.6 0.3 - - - +
42B TYR* 3.9 15.5 - - - -
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Residues in contact with GLN 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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160A HIS* 5.3 5.7 - - - -
17B GLU* 3.9 16.4 - - + +
18B THR* 2.9 14.9 + - - +
19B VAL 2.8 1.4 - - - -
20B GLY* 1.3 97.4 + - - +
22B PHE* 1.3 66.1 + - + +
23B PRO* 3.6 4.0 - - - +
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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