Contacts of the helix formed by residues 3 - 24 (chain L) in PDB entry 5MS0
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 PRO 3 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L GLU* 1.3 79.9 - - - +
4L ALA* 1.3 61.3 + - - +
5L ALA* 3.1 16.1 + - + +
6L ARG* 3.4 17.6 + - + +
7L ARG* 4.0 2.9 + - - +
7R A 5.9 0.2 - - - -
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Residues in contact with ALA 4 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L PRO* 1.3 72.1 - - - +
5L ALA* 1.3 59.1 + - - +
6L ARG 3.2 0.4 - - - -
7L ARG* 3.1 14.2 + - + +
8L ARG* 2.9 27.0 + - - +
42L ASP* 5.8 0.9 - - - -
7R A 5.9 1.3 - - - -
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Residues in contact with ALA 5 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L PRO* 3.1 10.4 - - + +
4L ALA* 1.3 77.5 - - - +
6L ARG* 1.3 56.9 + - - +
8L ARG 3.8 0.2 - - - -
9L ALA* 2.9 26.5 + - - +
42L ASP* 3.2 41.6 - - + +
43L VAL 4.0 2.7 - - - +
44L ASP* 3.3 14.5 + - + +
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Residues in contact with ARG 6 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L GLU* 4.6 14.1 - - + -
3L PRO* 3.4 13.1 + - + +
4L ALA 3.2 0.6 - - - -
5L ALA* 1.3 78.0 - - - +
7L ARG* 1.3 57.4 + - - +
9L ALA* 3.0 8.9 + - - +
10L ARG* 3.0 28.6 + - - +
44L ASP* 4.3 13.0 - - + +
47L TYR* 5.9 5.2 - - + -
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Residues in contact with ARG 7 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L PRO 4.0 2.1 + - - +
4L ALA* 3.1 20.6 + - + +
6L ARG* 1.3 78.6 - - - +
8L ARG* 1.3 59.7 + - - +
10L ARG* 4.0 5.2 + - - +
11L GLU* 3.7 15.9 + - - +
106L GLU* 5.5 11.9 - - + -
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Residues in contact with ARG 8 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4L ALA 2.9 12.2 + - - +
5L ALA* 4.5 0.2 - - - -
7L ARG* 1.3 76.1 - - - +
9L ALA* 1.3 59.0 + - - +
10L ARG 3.3 0.9 - - - -
11L GLU* 3.1 10.2 + - + +
12L CYS* 2.9 27.2 + - - +
40L VAL* 5.6 6.3 - - + +
42L ASP* 3.4 25.4 - - + +
43L VAL* 5.3 1.3 - - - +
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Residues in contact with ALA 9 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5L ALA 2.9 19.4 + - - +
6L ARG* 3.0 11.8 + - - +
8L ARG* 1.3 75.8 - - - +
10L ARG* 1.3 59.7 + - - +
12L CYS* 3.5 7.6 + - - +
13L ALA* 2.9 26.7 + - - +
43L VAL* 4.4 7.4 - - + -
44L ASP* 3.8 26.0 - - + +
47L TYR* 5.9 2.2 - - + -
48L PHE* 4.8 13.8 - - + +
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Residues in contact with ARG 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L ARG 3.0 13.3 + - - +
7L ARG* 4.5 5.6 - - - +
8L ARG 3.3 0.4 - - - -
9L ALA* 1.3 75.9 - - - +
11L GLU* 1.3 57.1 + - - +
13L ALA* 3.0 21.7 + - + +
14L VAL* 3.0 17.8 + - - +
107L ALA* 6.0 6.1 - - + -
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Residues in contact with GLU 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L ARG 3.7 12.6 + - - +
8L ARG* 3.1 14.3 + - + +
10L ARG* 1.3 79.8 - - - +
12L CYS* 1.3 59.9 + - - +
13L ALA 3.6 0.2 + - - -
14L VAL* 4.0 4.3 + - - +
15L GLN* 3.9 14.2 + - - +
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Residues in contact with CYS 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L ARG 2.9 14.5 + - - +
9L ALA* 3.9 7.6 - - - +
11L GLU* 1.3 75.7 - - - +
13L ALA* 1.3 58.3 + - - +
14L VAL 3.4 0.4 - - - -
15L GLN* 3.3 7.8 + - - +
16L ALA* 2.9 29.4 + - - +
43L VAL* 5.6 7.0 - - + -
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Residues in contact with ALA 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ALA 2.9 19.5 + - - +
10L ARG* 3.0 13.1 + - + +
12L CYS* 1.3 76.3 - - - +
14L VAL* 1.3 61.9 + - - +
16L ALA* 3.8 5.6 - - - +
17L LEU* 2.9 31.6 + - - +
48L PHE* 5.8 8.5 - - + +
51L LEU* 5.8 8.7 - - + -
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Residues in contact with VAL 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PRO* 6.0 0.8 - - - +
10L ARG 3.0 13.1 + - - +
11L GLU* 4.0 4.9 + - - +
13L ALA* 1.3 75.1 - - - +
15L GLN* 1.3 58.2 + - - +
17L LEU* 4.1 4.6 - - - +
18L TYR* 2.9 28.9 + - - +
80L VAL 5.9 0.4 - - - +
83L ALA* 4.5 18.9 - - + +
84L VAL* 5.8 3.4 - - + +
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Residues in contact with GLN 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E PRO 3.9 4.5 - - - +
40E ILE* 4.1 23.4 - - + +
41E PRO* 4.4 17.0 - - + +
11L GLU 3.9 10.8 + - - +
12L CYS* 3.3 10.6 + - - +
13L ALA 3.2 0.2 - - - -
14L VAL* 1.3 78.0 - - - +
16L ALA* 1.3 63.1 + - - +
18L TYR* 3.6 6.3 + - - +
19L SER* 3.3 20.6 + - - -
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Residues in contact with ALA 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L CYS 2.9 17.8 + - - +
13L ALA* 4.1 6.1 - - - +
15L GLN* 1.3 77.0 - - - +
17L LEU* 1.3 60.7 + - - +
19L SER* 3.6 7.1 + - - -
20L TRP* 3.4 18.9 + - - +
30L VAL* 5.5 3.6 - - - +
31L GLU* 6.1 3.6 - - + -
34L PHE* 4.6 20.4 - - + -
52L LEU* 6.2 4.0 - - + -
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Residues in contact with LEU 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L ALA 2.9 20.5 + - - +
14L VAL* 4.1 5.6 - - - +
16L ALA* 1.3 77.0 - - - +
18L TYR* 1.3 59.0 + - - +
19L SER 3.2 0.4 - - - -
20L TRP* 3.4 5.7 + - - +
21L GLN* 3.0 29.9 + - - +
55L VAL* 6.4 1.8 - - + -
83L ALA* 4.7 14.4 - - + +
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Residues in contact with TYR 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E PRO 4.0 7.6 - - - +
41E PRO* 5.1 12.1 - - + -
14L VAL 2.9 20.5 + - - +
15L GLN* 3.8 7.4 - - - +
16L ALA 3.4 0.2 - - - -
17L LEU* 1.3 77.5 - - - +
19L SER* 1.3 55.2 + - - +
21L GLN* 3.8 6.2 - - - +
22L LEU* 2.9 32.1 + - - +
79L GLN 6.1 0.7 - - - +
80L VAL* 6.4 1.8 - - - -
83L ALA* 4.9 7.3 - - + +
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Residues in contact with SER 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E GLY* 3.7 20.2 - - - -
39E PRO 3.3 21.7 + - - -
40E ILE* 5.5 0.7 - - - -
15L GLN 3.3 12.0 + - - -
16L ALA* 3.7 8.7 - - - -
17L LEU 3.2 0.6 - - - -
18L TYR* 1.3 79.8 - - - +
20L TRP* 1.3 57.1 + - - +
23L SER* 2.9 35.2 + - - +
30L VAL* 5.0 12.7 - - - +
34L PHE* 6.1 2.7 - - - -
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Residues in contact with TRP 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L ALA 3.4 10.0 + - - +
17L LEU* 3.4 8.4 + - - +
18L TYR 3.3 0.2 - - - -
19L SER* 1.3 76.2 - - - +
21L GLN* 1.3 65.5 + - - +
23L SER* 5.0 0.4 - - - -
24L GLN* 3.3 22.4 + - - +
25L ASN 4.6 7.6 + - - +
27L ILE* 5.5 10.3 - - + -
30L VAL* 4.7 16.1 - - + +
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Residues in contact with GLN 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L LEU 3.0 18.1 + - - +
18L TYR* 3.4 7.6 + - - +
20L TRP* 1.3 77.3 - - - +
22L LEU* 1.3 60.1 + - + +
24L GLN* 4.7 3.8 + - - +
79L GLN 6.1 0.9 - - - +
82L LYS* 6.5 0.7 - - + -
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Residues in contact with LEU 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E THR* 5.7 7.2 - - - +
23E ALA* 6.0 3.7 - - - +
26E VAL* 4.2 19.4 - - + +
39E PRO* 5.1 13.7 - - + -
18L TYR 2.9 17.3 + - - +
19L SER* 4.5 2.0 - - - +
21L GLN* 1.3 79.8 - - + +
23L SER* 1.3 64.4 + - - +
24L GLN* 3.3 5.0 + - - +
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Residues in contact with SER 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E VAL* 5.1 5.8 - - - -
36E VAL* 4.4 24.3 - - - +
38E GLY 3.4 16.2 - - - -
19L SER 2.9 21.2 + - - -
20L TRP* 5.0 0.4 - - - -
22L LEU* 1.3 78.8 - - - +
24L GLN* 1.3 67.2 + - - +
25L ASN* 3.3 14.8 + - - +
30L VAL* 5.7 4.0 - - - -
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Residues in contact with GLN 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L TRP 3.3 17.2 + - - -
21L GLN 5.2 2.7 - - - +
22L LEU 3.3 5.9 - - - +
23L SER* 1.3 77.9 - - - +
25L ASN* 1.3 62.1 + - - +
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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