Contacts of the helix formed by residues 2 - 22 (chain P) in PDB entry 5GAG
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 ASP 2 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B A 3.5 37.6 - - - +
60B C 4.0 12.2 + - - +
1P MET* 1.3 77.2 - - - +
3P LYS* 1.3 64.5 + - - +
4P LYS* 3.3 6.1 + - + +
5P SER* 2.3 55.5 + - - -
6P ALA 3.9 0.2 + - - -
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Residues in contact with LYS 3 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B C 2.8 36.7 + - - +
46B A 4.5 28.1 + - - +
47B C 3.3 34.7 + - - +
1P MET 3.8 4.1 + - - +
2P ASP* 1.3 71.9 - - - +
4P LYS* 1.3 63.7 + - - +
6P ALA* 3.0 10.9 + - - +
7P ARG* 3.0 22.3 + - - +
10P ARG* 5.0 1.2 + - - -
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Residues in contact with LYS 4 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B G 4.2 23.1 + - - +
8B C 5.5 4.7 + - - -
60B C 5.6 10.8 + - - -
61B G 5.9 0.4 + - - -
2P ASP* 3.1 6.8 + - + +
3P LYS* 1.3 78.0 - - - +
5P SER* 1.3 65.7 + - - +
7P ARG* 3.1 37.3 + - - +
8P ILE* 2.9 40.9 + - + +
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Residues in contact with SER 5 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1P MET* 3.3 22.7 - - - +
2P ASP* 2.3 43.1 + - - -
4P LYS* 1.3 75.6 - - - +
6P ALA* 1.3 60.8 + - - +
8P ILE* 3.1 18.5 + - - +
9P ARG* 2.9 20.6 + - - +
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Residues in contact with ALA 6 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2295A C 4.8 2.5 - - - +
2296A U 5.4 1.6 - - - +
1P MET* 3.5 18.7 - - + -
2P ASP 4.8 0.2 - - - +
3P LYS* 3.0 13.6 + - - +
5P SER* 1.3 79.5 + - - +
7P ARG* 1.3 65.3 + - - +
9P ARG* 3.0 25.8 + - - +
10P ARG* 2.9 39.8 + - - +
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Residues in contact with ARG 7 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B G 4.3 3.0 + - - -
8B C 4.2 15.2 + - - -
3P LYS 3.0 11.9 + - - +
4P LYS* 3.3 44.2 + - - +
6P ALA* 1.3 75.6 - - - +
8P ILE* 1.3 70.8 + - - +
10P ARG* 3.0 35.7 + - - +
11P ALA* 3.0 20.4 + - - +
15P ARG* 5.5 0.2 - - - +
29P HIS* 3.8 23.7 + - - -
95P SER* 3.5 20.9 + - - +
96P GLY* 4.0 5.0 - - - -
97P PHE* 3.3 47.1 - - - -
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Residues in contact with ILE 8 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P LYS* 2.9 41.2 + - + +
5P SER* 3.2 18.2 - - - +
7P ARG* 1.3 86.4 - - - +
9P ARG* 1.3 65.1 + - - +
11P ALA* 2.8 18.3 + - + +
12P THR* 2.9 19.1 + - - +
15P ARG* 5.6 8.3 - - - +
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Residues in contact with ARG 9 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2295A C 3.5 45.2 + - - -
2296A U 3.4 51.3 + - - -
2333A A 5.2 6.7 - - - -
2334A U 3.8 33.1 - - - +
2335A A 4.2 10.1 + - - +
1P MET* 5.2 10.1 - - + +
5P SER 2.9 12.1 + - - +
6P ALA* 3.2 30.9 + - - +
8P ILE* 1.3 76.7 - - - +
10P ARG* 1.3 73.2 + - - +
12P THR* 3.2 21.3 + - - -
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Residues in contact with ARG 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2294A G 3.3 35.1 + - - +
2295A C 3.2 41.8 + - - +
2335A A 5.4 2.9 + - - -
47B C 5.0 21.2 + - - -
3P LYS 5.0 1.0 + - - -
6P ALA* 2.9 22.2 + - - +
7P ARG* 3.0 47.5 + - - +
9P ARG* 1.3 84.5 - - - +
11P ALA* 1.3 62.1 + - - +
12P THR 3.3 0.9 + - - -
13P ARG* 4.1 9.9 + - - +
14P ALA* 4.8 2.4 + - - +
94P ARG* 5.8 2.5 + - - +
96P GLY* 3.2 26.9 + - - -
97P PHE* 5.3 2.8 - - - +
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Residues in contact with ALA 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P ARG 3.0 6.8 + - - +
8P ILE* 2.8 12.1 + - + +
10P ARG* 1.3 75.3 - - - +
12P THR* 1.3 63.6 + - - +
13P ARG 3.4 0.4 - - - -
14P ALA* 3.2 9.6 + - - +
15P ARG* 3.0 45.7 + - + +
93P ASP* 4.9 0.2 - - - +
95P SER* 3.4 36.3 - - - +
96P GLY* 4.1 5.6 - - - +
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Residues in contact with THR 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2334A U 3.4 46.9 + - + +
8P ILE* 2.9 22.4 + - - +
9P ARG* 3.2 15.5 + - - -
11P ALA* 1.3 75.5 - - - +
13P ARG* 1.3 64.2 + - - +
15P ARG* 3.4 6.9 + - - +
16P ARG* 2.9 39.2 + - + +
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Residues in contact with ARG 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2334A U 3.0 63.5 + - - +
2335A A 3.4 26.9 + - - +
2336A A 2.9 21.7 + - - -
10P ARG 4.1 7.4 + - - +
11P ALA 3.4 0.4 - - - -
12P THR* 1.3 77.5 - - - +
14P ALA* 1.3 63.8 + - - +
16P ARG* 3.3 2.9 + - - +
17P LYS* 3.0 24.8 + - + +
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Residues in contact with ALA 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2378A A 4.9 13.6 - - + +
10P ARG 4.8 2.4 + - - +
11P ALA* 3.2 12.0 + - - +
13P ARG* 1.3 79.0 - - - +
15P ARG* 1.3 58.8 + - - +
17P LYS* 3.1 7.4 + - - +
18P LEU* 2.9 36.6 + - + +
93P ASP* 4.1 14.6 - - - +
94P ARG* 6.3 2.9 - - + -
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Residues in contact with ARG 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B C 2.9 38.9 + - - -
9B G 2.6 43.0 + - - +
7P ARG* 5.5 0.2 - - - +
8P ILE* 5.6 7.7 - - - +
11P ALA* 3.0 31.1 + - - +
12P THR* 3.9 5.8 - - - +
14P ALA* 1.3 74.8 - - - +
16P ARG* 1.3 74.5 + - - +
18P LEU* 3.8 5.5 - - - +
19P GLN* 2.9 25.8 + - - +
25P ARG* 3.4 14.1 + - - +
27P VAL* 4.3 4.8 - - - +
93P ASP* 3.1 26.9 + - - +
95P SER* 2.8 27.5 + - - -
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Residues in contact with ARG 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2334A U 3.5 48.2 + - + +
9B G 5.4 7.9 + - - -
10B G 5.1 10.6 + - - -
12P THR* 2.9 31.8 + - + +
13P ARG 3.4 4.9 - - - +
15P ARG* 1.3 87.9 + - - +
17P LYS* 1.3 62.9 + - - +
19P GLN* 3.3 26.8 + - - +
20P GLU* 2.9 24.6 + - - +
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Residues in contact with LYS 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2378A A 4.3 20.2 - - + +
2379A G 4.0 17.3 - - - +
2380A C 3.2 36.2 + - - -
13P ARG* 3.0 14.6 + - + +
14P ALA* 3.5 9.9 - - - +
16P ARG* 1.3 75.7 - - - +
18P LEU* 1.3 64.1 + - - +
20P GLU* 3.0 34.0 + - - +
21P LEU* 2.9 40.6 + - + +
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Residues in contact with LEU 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2378A A 3.4 34.3 - - + +
14P ALA* 2.9 22.1 + - + +
15P ARG* 3.8 4.5 - - - +
17P LYS* 1.3 76.9 - - - +
19P GLN* 1.3 63.8 + - - +
21P LEU* 3.4 9.0 + - + +
22P GLY 3.3 3.3 + - - -
23P ALA* 3.2 30.4 + - + +
25P ARG* 4.0 25.8 - - + -
91P SER* 3.6 29.2 - - - +
92P PHE 4.4 5.6 - - - +
93P ASP* 4.0 33.0 - - + +
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Residues in contact with GLN 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B G 5.6 4.1 + - - -
15P ARG 2.9 16.1 + - - +
16P ARG* 3.3 39.4 + - - +
18P LEU* 1.3 77.2 - - - +
20P GLU* 1.3 57.8 + - - +
22P GLY* 2.8 23.2 + - - -
23P ALA 5.5 1.3 - - - -
42P PRO 5.2 12.3 - - - +
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Residues in contact with GLU 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2380A C 4.7 3.1 + - - -
16P ARG 2.9 12.2 + - - +
17P LYS* 3.0 44.9 + - - +
19P GLN* 1.3 79.8 - - - +
21P LEU* 1.3 69.6 + - + +
22P GLY* 3.3 1.0 + - - -
48X GLY 5.7 5.2 - - - +
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Residues in contact with LEU 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2378A A 3.8 17.7 - - + +
2379A G 3.5 34.5 - - - +
2380A C 4.5 11.0 - - - +
17P LYS* 2.9 32.9 + - + +
18P LEU* 3.8 14.4 - - + +
20P GLU* 1.3 91.4 - - - +
22P GLY* 1.3 60.3 + - - +
23P ALA* 4.3 7.9 - - + +
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Residues in contact with GLY 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P GLN* 2.8 17.6 + - - -
20P GLU 3.1 1.3 - - - -
21P LEU* 1.3 80.3 - - - +
23P ALA* 1.3 60.9 + - - +
24P THR 4.0 0.2 + - - -
42P PRO* 3.9 23.4 - - - +
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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
------------------------------------------------------------
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