Contacts of the helix formed by residues 19 - 37 (chain P) in PDB entry 1HH2
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 19 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P GLY 4.0 3.4 + - - -
18P ILE* 1.3 70.6 - - - +
20P LYS* 1.3 55.0 + - - +
21P GLU* 2.7 35.8 + - - +
22P GLU* 3.4 10.2 + - - +
23P VAL* 3.7 7.5 - - - +
117P ARG* 4.9 6.5 + - - +
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Residues in contact with LYS 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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8P ALA* 4.2 15.0 - - - +
11P GLN* 3.0 60.2 - - + +
18P ILE 3.3 1.8 + - - -
19P SER* 1.3 67.5 + - - +
21P GLU* 1.3 55.8 + - - +
22P GLU 2.8 10.4 + - - -
23P VAL* 3.5 28.6 + - + -
24P ILE* 3.4 37.5 - - + +
51P ARG* 5.5 0.3 + - - -
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Residues in contact with GLU 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P SER* 2.7 23.9 + - - +
20P LYS* 1.3 74.8 - - - +
22P GLU* 1.3 64.3 + - + +
24P ILE* 5.2 0.4 - - - -
25P PRO* 3.9 9.8 - - - +
51P ARG* 3.7 19.3 + - - +
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Residues in contact with GLU 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P SER 3.4 4.2 + - - +
21P GLU* 1.3 88.2 - - + +
23P VAL* 1.3 65.6 + - - +
25P PRO* 3.0 21.6 - - - +
26P ILE* 3.0 38.6 - - + +
117P ARG* 3.4 37.0 - - - +
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Residues in contact with VAL 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P GLN* 5.2 0.9 - - - +
18P ILE* 3.5 31.0 - - + -
19P SER 3.7 2.9 - - - +
20P LYS* 3.5 33.1 + - + -
22P GLU* 1.3 79.1 - - + +
24P ILE* 1.3 57.9 + - + +
26P ILE* 3.7 4.7 + - - +
27P LEU* 3.0 35.1 + - + +
113P VAL* 4.4 4.1 - - + +
114P LEU* 3.3 36.3 - - + -
117P ARG* 5.1 16.1 - - + +
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Residues in contact with ILE 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P GLU* 5.3 3.1 - - - +
20P LYS* 3.4 32.3 + - + +
23P VAL* 1.3 75.0 - - + +
25P PRO* 1.3 78.1 - - + +
26P ILE 3.0 2.0 - - - -
27P LEU* 2.8 11.9 + - + +
28P GLU* 2.6 42.5 + - - +
49P ILE* 3.5 38.6 - - + +
51P ARG* 3.1 50.9 - - + +
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Residues in contact with PRO 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P GLU 3.9 13.7 - - - +
22P GLU* 3.0 33.9 - - - +
24P ILE* 1.3 103.4 - - + +
26P ILE* 1.3 59.0 + - + +
28P GLU* 3.6 17.2 - - - +
29P LYS* 3.0 31.6 + - - +
51P ARG* 4.8 6.7 - - - +
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Residues in contact with ILE 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P GLU* 3.0 41.0 + - + +
23P VAL* 3.9 5.2 - - - +
24P ILE 3.0 0.4 - - - -
25P PRO* 1.3 76.3 - - + +
27P LEU* 1.3 67.1 + - - +
29P LYS* 3.3 13.2 + - + +
30P ALA* 2.9 23.4 + - + +
113P VAL* 3.7 20.4 - - + -
117P ARG* 5.8 7.6 - - + -
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Residues in contact with LEU 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P GLU* 3.2 28.5 - - - +
23P VAL* 3.0 31.6 + - + +
24P ILE* 2.8 16.0 + - + +
26P ILE* 1.3 77.4 - - - +
28P GLU* 1.3 51.1 + - - +
30P ALA* 3.2 2.8 + - + +
31P LEU* 2.6 54.2 + - + +
49P ILE* 5.1 2.2 - - + -
109P THR* 5.8 0.2 - - - +
110P ALA* 3.2 44.6 - - + +
113P VAL* 3.3 25.8 - - + -
114P LEU* 4.9 3.8 - - + -
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Residues in contact with GLU 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P ILE* 2.6 26.6 + - - +
25P PRO* 3.6 18.6 - - - +
27P LEU* 1.3 71.9 - - - +
29P LYS* 1.3 54.1 + - + +
31P LEU* 3.0 11.3 + - - +
32P VAL* 2.8 39.5 + - - +
47P VAL* 3.4 24.7 - - + +
48P VAL* 3.7 5.2 - - - +
49P ILE* 3.0 47.9 + - + +
51P ARG* 4.9 2.9 + - - -
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Residues in contact with LYS 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P PRO* 3.0 23.5 + - - +
26P ILE* 3.5 16.4 - - + +
28P GLU* 1.3 80.0 - - + +
30P ALA* 1.3 63.3 + - - +
32P VAL* 3.2 15.7 + - - +
33P SER* 3.3 14.8 + - - -
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Residues in contact with ALA 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P ILE* 2.9 18.8 + - + +
27P LEU* 3.6 3.8 - - + +
29P LYS* 1.3 72.4 - - - +
31P LEU* 1.3 55.5 + - + +
33P SER* 3.0 10.8 + - - -
34P ALA* 2.6 36.2 + - - +
109P THR* 5.3 5.4 - - - +
113P VAL* 3.6 26.7 - - + -
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Residues in contact with LEU 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1P MET 4.0 21.9 + - - +
7P GLU* 5.6 0.7 - - - +
27P LEU* 2.6 51.3 + - + +
28P GLU* 3.3 9.6 - - - +
30P ALA* 1.3 69.1 - - + +
32P VAL* 1.3 57.3 + - - +
34P ALA* 3.3 7.2 - - + +
35P TYR* 2.6 36.4 + - - +
47P VAL* 3.9 19.9 - - + +
49P ILE* 4.0 19.1 - - + -
56P ILE* 4.3 16.8 - - + -
107P ALA* 4.7 11.9 - - - +
109P THR* 4.4 14.6 - - - +
110P ALA* 5.4 4.5 - - + -
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Residues in contact with VAL 32 (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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28P GLU 2.8 22.8 + - - +
29P LYS* 3.4 10.3 - - - +
30P ALA 3.2 0.4 - - - -
31P LEU* 1.3 72.7 - - - +
33P SER* 1.3 60.3 + - - +
35P TYR* 3.3 5.4 + - - +
36P ARG* 3.0 30.2 + - + +
45P VAL* 3.8 29.4 - - + +
46P GLU* 4.3 1.8 - - + -
47P VAL* 3.7 32.1 - - + +
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Residues in contact with SER 33 (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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29P LYS 3.3 8.9 + - - -
30P ALA* 3.0 12.4 + - - -
32P VAL* 1.3 79.3 - - - +
34P ALA* 1.3 57.2 + - - +
36P ARG* 3.2 19.2 + - - +
37P LYS* 3.0 30.1 + - - +
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Residues in contact with ALA 34 (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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1P MET* 4.8 2.9 - - + -
30P ALA 2.6 18.5 + - - +
31P LEU* 3.0 17.0 + - + +
33P SER* 1.3 71.2 - - - +
35P TYR* 1.3 64.9 + - - +
36P ARG 3.2 0.3 + - - -
37P LYS* 3.3 9.5 - - - +
38P ASN* 3.2 22.6 - - - +
106P ALA* 4.5 12.4 - - + +
109P THR* 3.9 27.4 - - + +
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Residues in contact with TYR 35 (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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1P MET* 3.7 39.4 - - + +
31P LEU 2.6 19.5 + - - +
32P VAL* 3.5 5.6 - - - +
34P ALA* 1.3 73.8 - - - +
36P ARG* 1.3 67.2 + - - +
38P ASN 3.7 4.7 + - - -
39P PHE* 3.7 46.4 - + + +
40P GLY 5.0 4.0 - - - -
43P LYS* 4.5 6.9 + - + +
45P VAL* 3.8 31.9 - - + -
47P VAL* 5.1 3.8 - - + -
58P VAL* 4.0 32.8 - - + -
97P LEU* 3.5 23.6 - - + +
98P ASN 5.6 3.1 - - - -
100P LYS* 5.8 6.2 - - + +
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Residues in contact with ARG 36 (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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32P VAL* 3.0 16.7 + - + +
33P SER* 3.2 20.5 + - - +
35P TYR* 1.3 81.0 - - - +
37P LYS* 1.3 105.0 + - - +
38P ASN 2.7 8.7 + - - -
39P PHE 3.9 0.3 - - - -
40P GLY* 3.3 27.6 + - - +
41P ASN* 3.0 43.4 + - + +
45P VAL* 6.1 0.4 - - + -
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Residues in contact with LYS 37 (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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33P SER 3.0 12.9 + - - +
34P ALA* 3.3 6.1 - - - +
36P ARG* 1.3 107.4 - - - +
38P ASN* 1.3 69.6 + - - +
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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
------------------------------------------------------------
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