Contacts of the helix formed by residues 4 - 19 (chain H) in PDB entry 4ADV
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 4 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877A G 2.9 43.7 + - + +
1H SER* 3.3 18.9 + - - -
3H GLN* 1.3 78.0 - - - +
5H PRO* 1.3 64.9 - - - +
6H ILE* 3.3 4.4 + - - +
7H ALA* 3.5 22.6 + - + +
8H ASP* 3.3 13.3 + - - +
76H ARG* 3.6 15.0 + - - -
79H ARG* 4.4 0.5 - - - +
80H PRO* 2.9 30.4 - - + +
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Residues in contact with PRO 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A G 3.3 34.5 - - - +
589A U 3.2 19.7 - - - +
1H SER 3.4 18.1 + - - +
3H GLN 3.5 2.0 - - - +
4H ASP* 1.3 87.6 - - - +
6H ILE* 1.3 69.7 + - + +
8H ASP* 3.7 4.2 - - - +
9H MET* 3.5 12.6 + - - +
32H LYS* 3.0 41.2 - - - +
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Residues in contact with ILE 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ASP* 3.3 2.0 - - - +
5H PRO* 1.3 83.2 - - + +
7H ALA* 1.3 66.1 + - - +
8H ASP 3.1 1.3 - - - -
9H MET* 3.1 20.5 + - + +
10H LEU* 3.6 11.5 + - + +
29H SER* 4.9 0.9 - - - +
31H LEU* 3.4 44.0 - - + -
32H LYS* 3.9 26.2 - - + +
35H ILE* 3.8 22.0 - - + -
76H ARG* 3.6 28.3 - - + +
125H ILE* 4.4 9.0 - - + -
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Residues in contact with ALA 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A C 4.0 2.0 + - - +
877A G 3.7 28.3 - - - +
4H ASP* 3.5 29.4 + - + +
5H PRO 3.5 0.2 - - - -
6H ILE* 1.3 79.3 - - - +
8H ASP* 1.3 60.1 + - - +
10H LEU* 3.5 12.5 + - - +
11H THR* 2.9 26.2 + - - -
14H ARG* 4.8 0.5 + - - -
76H ARG* 3.3 18.3 - - + +
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Residues in contact with ASP 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A A 3.3 25.7 + - - +
1H SER* 3.3 35.5 + - - +
4H ASP 3.3 5.0 + - - +
5H PRO 3.7 4.9 - - - +
6H ILE 3.1 0.2 - - - -
7H ALA* 1.3 77.1 - - - +
9H MET* 1.3 66.3 + - - +
11H THR* 3.1 7.5 + - - -
12H ARG* 2.8 70.7 + - - +
26H MET* 4.5 5.0 - - - +
27H PRO* 5.1 3.8 - - - +
32H LYS* 5.7 1.0 - - - -
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Residues in contact with MET 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H PRO 3.5 9.1 + - - +
6H ILE* 3.1 13.1 + - - +
8H ASP* 1.3 79.8 + - - +
10H LEU* 1.3 68.5 + - + +
12H ARG* 3.4 2.4 + - - +
13H ILE* 3.0 41.4 + - + +
26H MET* 3.7 19.0 - - + +
32H LYS* 2.9 56.1 - - + +
35H ILE* 3.9 28.3 - - - -
36H ALA* 3.9 12.8 - - + -
39H LEU* 5.9 0.4 - - - -
58H LEU* 3.6 16.8 - - + -
60H LEU* 4.7 5.8 - - + -
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Residues in contact with LEU 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ILE* 3.8 17.0 - - + +
7H ALA 3.8 4.9 - - - +
8H ASP 3.3 0.6 - - - -
9H MET* 1.3 86.4 - - + +
11H THR* 1.3 58.6 + - - +
13H ILE* 3.0 5.7 + - + +
14H ARG* 2.8 39.8 + - - +
35H ILE* 5.3 4.0 - - + -
39H LEU* 6.4 2.2 - - + -
74H ILE* 3.3 30.5 - - + +
75H GLN 3.9 2.7 - - - -
76H ARG* 3.6 42.4 - - + +
125H ILE* 6.0 0.2 - - + -
126H CYS* 3.6 36.8 - - + -
128H VAL* 5.8 0.2 - - + -
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Residues in contact with THR 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A A 4.3 9.4 - - + +
826A C 5.3 0.4 - - - -
875A U 3.2 14.6 - - - +
876A C 2.9 26.5 + - - -
7H ALA 2.9 15.1 + - - -
8H ASP* 3.1 12.7 + - - -
10H LEU* 1.3 78.0 - - - +
12H ARG* 1.3 53.3 + - - +
14H ARG* 2.9 24.2 + - - +
15H ASN* 2.7 62.1 + - - +
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Residues in contact with ARG 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825A A 3.3 20.7 + - - +
826A C 3.2 50.9 + - - +
8H ASP* 2.8 53.9 + - - +
11H THR* 1.3 73.4 - - - +
13H ILE* 1.3 60.7 + - - +
15H ASN* 4.2 0.7 - - - +
16H GLY* 3.1 18.4 + - - -
24H VAL* 3.5 19.0 - - + +
25H THR 3.4 15.0 + - - -
26H MET* 3.3 49.1 - - + +
27H PRO* 3.9 10.5 - - - +
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Residues in contact with ILE 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H MET* 3.0 32.5 + - + +
10H LEU* 3.0 9.4 + - + +
12H ARG* 1.3 75.6 - - - +
14H ARG* 1.3 65.0 + - - +
16H GLY* 3.4 1.6 + - - -
17H GLN* 3.1 31.3 + - + +
24H VAL* 4.3 12.3 - - + -
26H MET* 4.9 1.3 - - + -
36H ALA* 6.4 0.4 - - - -
39H LEU* 4.9 18.2 - - + -
45H ILE* 5.6 8.1 - - + -
60H LEU* 3.6 32.5 - - + -
62H LEU* 4.5 8.9 - - + +
71H VAL* 4.7 15.0 - - + -
74H ILE* 4.1 18.8 - - + -
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Residues in contact with ARG 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A U 2.9 28.4 + - - +
876A C 3.5 15.0 + - - -
7H ALA 4.8 0.6 + - - -
10H LEU* 2.8 29.4 + - - +
11H THR* 2.9 50.9 + - - +
13H ILE* 1.3 71.7 - - - +
15H ASN* 1.3 70.1 + - - +
17H GLN* 3.4 8.9 + - - +
18H ALA* 3.2 22.5 + - - +
71H VAL 5.6 0.9 - - - +
74H ILE* 3.0 50.1 + - + -
75H GLN* 3.0 30.9 + - - +
76H ARG* 4.8 1.8 - - - +
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Residues in contact with ASN 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A C 2.7 52.8 + - + +
827A U 4.2 12.2 + - - +
874A G 3.8 5.1 + - - -
875A U 2.9 40.8 + - - +
11H THR* 2.7 32.4 + - - +
12H ARG 4.2 0.4 - - - +
14H ARG* 1.3 73.2 - - - +
16H GLY* 1.3 62.8 + - - +
18H ALA* 3.6 6.6 + - - +
19H ALA* 3.4 19.6 + - - +
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Residues in contact with GLY 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826A C 5.0 0.2 + - - -
827A U 5.3 3.6 - - - -
12H ARG 3.1 18.1 + - - -
13H ILE 3.8 1.3 - - - -
15H ASN* 1.3 74.7 - - - +
17H GLN* 1.3 65.1 + - - +
19H ALA* 3.1 7.3 + - - -
21H LYS* 2.9 35.8 + - - +
24H VAL* 5.6 2.9 - - - -
62H LEU* 3.3 15.9 - - - -
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Residues in contact with GLN 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ILE* 3.1 21.8 + - + +
14H ARG* 3.5 9.9 - - - +
16H GLY* 1.3 73.6 - - - +
18H ALA* 1.3 55.7 + - - +
20H ASN* 2.6 33.3 + - - +
62H LEU* 3.5 22.0 - - + +
63H LYS 3.3 17.8 + - - +
64H TYR* 4.8 3.6 - - - -
69H ALA* 3.0 36.3 - - + +
71H VAL* 3.1 52.1 + - + +
72H GLU* 5.0 0.7 - - - +
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Residues in contact with ALA 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A A 5.5 3.1 + - - +
14H ARG 3.2 10.4 + - - +
15H ASN* 3.8 10.1 - - - +
16H GLY 3.3 0.2 - - - -
17H GLN* 1.3 78.7 - - - +
19H ALA* 1.3 57.0 + - - +
20H ASN* 3.0 14.4 + - - +
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Residues in contact with ALA 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A U 3.7 31.6 - - - +
828A U 4.3 4.3 - - - +
28B PRO* 4.8 0.2 - - + -
29B PHE* 4.1 24.7 - - + -
44B LYS* 4.9 2.9 - - - +
48B MET* 4.6 4.2 - - - +
15H ASN 3.4 9.7 + - - +
16H GLY 3.1 8.5 + - - +
18H ALA* 1.3 76.3 - - - +
20H ASN* 1.3 67.3 + - - +
21H LYS* 2.9 18.6 + - + +
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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
------------------------------------------------------------
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