Contacts of the helix formed by residues 1 - 19 (chain B) in PDB entry 3D10
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 1 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ASN 4.5 4.5 - - - -
39A GLU* 2.7 50.3 + - - -
42A HIS* 4.9 1.2 + - - -
0B MET* 1.3 74.5 - - - +
2B GLU* 1.3 64.4 + - - +
3B LEU* 3.4 2.3 + - - -
4B GLU* 2.9 24.4 + - - -
5B LYS* 2.9 20.8 + - - +
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Residues in contact with GLU 2 (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 ALA* 4.1 20.0 - - + +
13A VAL* 6.4 1.3 - - + -
39A GLU* 4.8 3.0 + - - -
0B MET 5.4 1.4 - - - +
1B SER* 1.3 73.3 - - - +
3B LEU* 1.3 57.0 + - - +
5B LYS* 3.3 30.4 + - - +
6B ALA* 2.9 30.4 + - - +
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Residues in contact with LEU 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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9A ALA* 5.2 1.5 - - - +
10A LEU* 3.5 30.7 - - + -
13A VAL* 3.9 29.7 - - + +
35A LEU* 4.1 14.6 - - + -
39A GLU* 4.1 19.0 + - + +
40A LEU* 3.7 35.0 - - + -
73A PHE* 4.5 9.6 - - + -
76A PHE* 6.1 0.2 - - + -
77A VAL* 4.6 1.6 - - + -
1B SER* 3.2 6.0 + - - +
2B GLU* 1.3 79.1 - - - +
4B GLU* 1.3 58.3 + - - +
6B ALA* 3.1 6.7 + - - +
7B MET* 2.9 41.4 + - + +
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Residues in contact with GLU 4 (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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39A GLU 3.3 17.3 - - - +
40A LEU* 3.1 15.7 - - + -
41A SER* 4.1 1.1 + - - -
42A HIS* 2.7 56.8 + - - +
43A PHE* 3.7 29.2 + - + -
0B MET* 3.8 15.2 - - + -
1B SER* 2.9 28.6 + - - +
3B LEU* 1.3 71.9 - - - +
5B LYS* 1.4 63.5 + - - +
7B MET* 3.3 3.9 + - - +
8B VAL* 3.1 28.8 + - - +
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Residues in contact with LYS 5 (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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2A GLU* 4.6 12.9 + - - -
5A LYS* 5.1 8.9 - - - +
0B MET* 3.5 37.1 - - + +
1B SER 2.9 14.0 + - - +
2B GLU* 3.3 39.7 + - - +
3B LEU 3.3 0.2 - - - -
4B GLU* 1.4 74.5 - - - +
6B ALA* 1.3 57.6 + - - +
8B VAL* 3.2 4.0 + - - +
9B ALA* 3.0 30.1 + - - +
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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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6A ALA* 3.6 40.0 - - + +
9A ALA* 4.0 7.9 - - + -
10A LEU* 4.0 12.8 - - + -
2B GLU 2.9 13.5 + - - +
3B LEU* 3.1 8.9 + - - +
5B LYS* 1.3 73.0 - - - +
7B MET* 1.3 67.0 + - - +
9B ALA* 3.2 4.5 + - - +
10B LEU* 3.0 27.7 + - - +
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Residues in contact with MET 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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10A LEU* 5.1 0.7 - - + -
40A LEU* 3.7 28.0 - - + -
43A PHE* 3.9 17.3 - - + -
76A PHE* 5.8 1.3 - - + -
77A VAL* 4.0 30.3 - - + -
80A VAL* 3.6 41.1 - - + -
81A THR* 3.3 25.1 - - + +
84A CYS* 6.5 0.2 - - + -
3B LEU* 2.9 28.7 + - + +
4B GLU 3.3 7.4 + - - +
6B ALA* 1.3 77.5 - - - +
8B VAL* 1.3 61.4 + - - +
10B LEU* 3.2 15.4 + - - +
11B ILE* 3.3 21.8 + - + +
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Residues in contact with VAL 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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43A PHE* 3.7 23.3 - - + -
84A CYS* 5.7 2.0 - - - -
0B MET* 4.4 15.9 - - + -
4B GLU 3.1 17.7 + - - +
5B LYS 3.2 4.5 + - - +
7B MET* 1.3 74.5 - - - +
9B ALA* 1.3 67.2 + - - +
11B ILE* 3.3 12.1 + - + +
12B ASP* 2.9 29.9 + - + +
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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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2A GLU* 4.2 24.7 - - + +
3A LEU* 5.3 0.7 - - - -
6A ALA* 4.0 16.2 - - + -
5B LYS* 3.0 15.0 + - - +
6B ALA* 3.5 9.0 - - - +
8B VAL* 1.3 78.2 - - - +
10B LEU* 1.3 56.1 + - - +
12B ASP* 4.3 6.3 - - - -
13B VAL* 2.9 37.1 + - - +
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Residues in contact with LEU 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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3A LEU* 3.4 30.7 - - + -
6A ALA* 4.2 9.6 - - + -
7A MET* 5.3 1.3 - - + -
10A LEU* 4.7 7.4 - - + -
77A VAL* 4.6 9.4 - - + -
81A THR* 4.4 11.7 - - + +
6B ALA 3.0 22.6 + - - +
7B MET* 3.6 9.0 - - - +
8B VAL 3.2 0.4 - - - -
9B ALA* 1.3 77.9 - - - +
11B ILE* 1.3 61.4 - - - +
13B VAL* 4.2 0.5 - - - +
14B PHE* 3.1 24.6 + - - +
70B PHE* 4.0 2.0 - - - -
73B PHE* 3.6 9.4 - - + -
74B MET* 3.6 39.9 - - + -
77B VAL* 3.9 25.4 - - + -
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Residues in contact with ILE 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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81A THR* 3.7 33.0 - - + +
84A CYS* 4.0 17.0 - - + -
85A HIS* 4.0 21.1 - - + +
89A GLU* 5.7 0.2 - - - +
7B MET* 3.3 17.5 + - + +
8B VAL* 3.3 10.7 + - + +
10B LEU* 1.3 76.5 - - - +
12B ASP* 1.3 63.1 + - - +
14B PHE* 3.4 0.7 + - - +
15B HIS* 2.8 52.3 + - + +
70B PHE* 3.8 15.7 - - + -
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Residues in contact with ASP 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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8B VAL* 2.9 22.9 + - + +
9B ALA* 3.7 6.7 - - - +
11B ILE* 1.3 76.3 - - - +
13B VAL* 1.3 67.3 + - - +
15B HIS* 3.3 6.1 + - - +
16B GLN* 2.8 48.1 + - - +
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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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2A GLU* 4.7 9.6 - - + -
3A LEU* 4.3 37.5 - - + +
9B ALA* 2.9 26.7 + - - +
10B LEU 4.3 1.8 - - - +
12B ASP* 1.3 71.6 - - + +
14B PHE* 1.3 64.4 + - - +
16B GLN* 3.1 33.2 + - - +
17B TYR* 3.2 13.8 + - + +
35B LEU* 4.1 18.2 - - + -
39B GLU* 4.1 25.1 - - + +
73B PHE* 5.2 1.3 - - + -
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Residues in contact with PHE 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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10B LEU 3.1 18.5 + - - +
11B ILE 3.5 4.0 - - - +
13B VAL* 1.3 76.9 - - - +
15B HIS* 1.3 70.5 + + - +
17B TYR* 3.3 1.4 + - - -
18B SER* 2.8 45.6 + - - -
25B HIS* 3.5 31.0 - + - -
27B LEU* 3.8 17.5 - - + +
35B LEU* 4.7 5.6 - - - -
68B CYS 3.7 12.1 - - - -
69B ASP 3.5 17.9 - - - -
70B PHE* 3.4 46.4 - + + -
73B PHE* 3.5 32.1 - + + -
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Residues in contact with HIS 15 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A HIS* 3.2 19.5 - + - -
89A GLU* 3.1 6.7 + - - -
95A ZN 2.0 36.8 - - - -
11B ILE* 2.8 37.0 + - + +
12B ASP* 3.3 5.4 + - - +
14B PHE* 1.3 89.0 - + - +
16B GLN* 1.3 67.4 + - - +
18B SER* 3.4 7.9 - - - -
19B GLY* 3.1 21.1 + - - -
24B LYS 4.9 3.7 - - - +
25B HIS* 3.4 9.6 + + - -
70B PHE* 5.0 0.7 - + - -
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Residues in contact with GLN 16 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B ASP* 2.8 49.7 + - - +
13B VAL* 3.2 24.8 - - - +
15B HIS* 1.3 80.4 - - - +
17B TYR* 1.3 76.2 + - + +
19B GLY 4.2 2.3 + - - -
20B ARG* 3.7 18.1 + - - +
39B GLU* 5.0 3.8 - - - +
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Residues in contact with TYR 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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13B VAL* 3.2 20.4 + - + +
15B HIS 3.1 0.4 - - - -
16B GLN* 1.3 89.1 - - + +
18B SER* 1.3 65.8 + - - +
19B GLY 3.3 2.2 - - - -
20B ARG* 3.2 47.1 + - - +
27B LEU* 3.4 19.1 - - + -
31B GLU* 3.0 31.5 - - - +
34B GLU* 3.6 5.2 - - + -
35B LEU* 3.4 41.7 - - + -
38B ASN* 3.2 16.8 + - - +
39B GLU* 2.5 46.0 + - + -
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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
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14B PHE* 2.8 37.1 + - - -
15B HIS* 3.4 10.7 - - - +
17B TYR* 1.3 79.8 - - - +
19B GLY* 1.3 56.5 + - - +
20B ARG 3.2 0.6 + - - -
23B ASP 3.0 8.5 - - - +
24B LYS* 3.0 13.5 + - - -
25B HIS* 3.9 0.5 - - - -
26B LYS 3.5 31.4 - - - -
27B LEU* 3.2 12.1 - - - +
31B GLU* 3.1 2.9 - - - +
92B CA 2.3 27.2 - - - -
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Residues in contact with GLY 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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15B HIS 3.1 16.0 + - - -
16B GLN 4.7 2.0 - - - -
17B TYR 3.3 0.2 - - - -
18B SER* 1.3 76.5 + - - +
20B ARG* 1.3 65.4 + - - +
21B GLU 3.4 1.3 - - - -
24B LYS* 3.6 38.6 + - - -
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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