Contacts of the helix formed by residues 22 - 35 (chain H) in PDB entry 3PHW
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 THR 22 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20H SER 3.4 2.6 + - - +
21H ASP* 1.3 76.5 - - - +
23H ILE* 1.3 64.4 + - - +
24H GLU* 3.7 7.2 + - - +
25H ASN* 2.9 46.0 + - - +
26H VAL* 3.0 12.9 + - - +
52H ASP 3.9 9.0 - - - -
53H GLY* 4.3 11.2 - - - +
54H ARG 3.0 14.8 - - - +
55H THR* 4.0 13.0 - - + +
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Residues in contact with ILE 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H THR* 1.3 71.8 - - - +
24H GLU* 1.3 63.8 + - - +
26H VAL* 3.0 7.8 + - + +
27H LYS* 2.9 47.3 + - - +
43H LEU* 3.7 13.5 - - + -
50H LEU* 3.7 44.6 - - + +
51H GLU 2.9 29.2 - - - +
52H ASP* 3.5 6.0 + - - +
54H ARG 2.9 11.6 + - - +
55H THR 4.7 2.2 - - - -
56H LEU* 4.3 17.0 - - + -
59H TYR* 4.4 11.0 - - + -
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Residues in contact with GLU 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H THR* 3.2 8.5 + - - +
23H ILE* 1.3 75.8 - - - +
25H ASN* 1.3 60.6 + - - +
27H LYS* 3.2 8.7 + - - +
28H ALA* 2.9 27.7 + - - +
38H PRO* 5.5 0.9 - - - +
52H ASP* 2.9 51.4 + - - +
53H GLY* 4.3 6.4 - - - -
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Residues in contact with ASN 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H SER 4.7 1.8 + - - -
21H ASP* 4.0 12.4 + - + +
22H THR* 2.9 43.4 + - - +
24H GLU* 1.3 75.8 - - - +
26H VAL* 1.3 65.7 + - - +
28H ALA* 3.2 8.2 + - - +
29H LYS* 3.0 43.9 + - - +
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Residues in contact with VAL 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 4.7 1.6 - - + -
15H LEU* 3.7 21.1 - - + -
17H VAL* 4.6 6.5 - - + -
21H ASP* 4.1 7.2 - - + -
22H THR 3.0 13.9 + - - +
23H ILE* 3.0 9.8 + - + +
25H ASN* 1.3 74.5 - - - +
27H LYS* 1.3 57.6 + - - +
29H LYS* 2.9 11.8 + - - +
30H ILE* 2.8 31.1 + - + +
43H LEU* 3.9 19.5 - - + -
56H LEU* 4.0 35.0 - - + -
67H LEU* 4.5 12.1 - - + -
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Residues in contact with LYS 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G LEU* 4.7 13.1 - - - +
23H ILE* 2.9 35.1 + - - +
24H GLU* 3.2 7.8 + - - +
26H VAL* 1.3 75.8 - - - +
28H ALA* 1.3 58.3 + - - +
30H ILE* 3.3 0.4 + - - -
31H GLN* 3.0 24.8 + - - +
38H PRO* 3.7 28.4 + - + +
41H GLN* 3.0 63.2 + - + +
42H ARG* 4.8 1.0 - - - +
43H LEU* 3.7 17.7 - - + +
50H LEU 5.1 5.6 + - - -
52H ASP* 3.5 22.9 + - - +
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Residues in contact with ALA 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 5.8 6.8 + - + +
24H GLU 2.9 12.7 + - - +
25H ASN* 3.5 11.9 - - - +
26H VAL 3.2 0.2 - - - -
27H LYS* 1.3 76.7 - - - +
29H LYS* 1.3 59.6 + - + +
31H GLN* 3.3 15.0 + - - +
32H ASP* 2.9 30.8 + - - +
38H PRO* 4.8 5.3 - - + +
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Residues in contact with LYS 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H LEU* 3.9 17.0 - - + +
16H GLU 3.4 23.8 - - - +
17H VAL* 4.1 8.1 - - + +
18H GLU* 6.1 1.6 - - - -
21H ASP* 3.3 34.2 + - - +
25H ASN* 3.0 28.2 + - - +
26H VAL* 2.9 9.0 + - - +
28H ALA* 1.3 74.5 - - + +
30H ILE* 1.3 60.2 + - - +
32H ASP* 3.3 7.7 + - - +
33H LYS* 2.9 29.8 + - - +
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Residues in contact with ILE 30 (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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5H VAL* 4.5 13.2 - - + -
7H THR* 6.2 0.4 - - + -
13H ILE* 4.9 6.3 - - + -
15H LEU* 3.7 21.3 - - + -
26H VAL* 2.8 26.0 + - + +
27H LYS* 3.6 7.2 - - - +
29H LYS* 1.3 74.3 - - - +
31H GLN* 1.3 55.5 + - - +
33H LYS* 4.4 1.8 - - - -
34H GLU* 2.6 40.7 + - + -
35H GLY 3.6 0.2 + - - -
36H ILE* 4.2 13.2 + - + -
41H GLN* 3.2 34.5 - - - +
43H LEU* 3.8 26.7 - - + -
69H LEU* 4.0 15.5 - - + -
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Residues in contact with GLN 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 3.2 52.1 + - - +
34A GLN 5.0 0.9 - - - +
147A SER* 4.5 4.8 + - - -
151A HIS* 3.3 33.2 + - - -
153A ASP* 3.3 1.6 + - - -
27H LYS 3.0 12.6 + - - +
28H ALA* 3.3 13.3 + - - +
30H ILE* 1.3 76.7 - - - +
32H ASP* 1.3 60.0 + - - +
35H GLY* 2.7 31.2 + - - -
36H ILE 3.5 26.4 + - - +
37H PRO* 4.3 3.0 - - - +
38H PRO* 3.5 22.1 - - + +
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Residues in contact with ASP 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 3.4 34.7 + - - +
28H ALA* 2.9 16.7 + - - +
29H LYS* 3.7 10.9 - - - +
30H ILE 3.3 0.2 - - - -
31H GLN* 1.3 77.0 - - - +
33H LYS* 1.3 63.1 + - - +
35H GLY 4.7 0.5 + - - -
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Residues in contact with LYS 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H ILE* 4.0 14.6 - - + -
14H THR* 3.1 38.6 + - - +
15H LEU* 4.1 11.0 - - + -
29H LYS 2.9 18.3 + - - +
30H ILE* 3.7 2.9 - - - +
32H ASP* 1.3 79.6 - - - +
34H GLU* 1.3 85.6 + - + +
35H GLY 3.7 0.2 - - - -
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Residues in contact with GLU 34 (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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7H THR* 5.0 3.7 - - + +
11H LYS* 2.9 40.1 + - - -
13H ILE* 3.6 36.7 - - + +
30H ILE* 2.6 17.8 + - + +
33H LYS* 1.3 96.9 - - + +
35H GLY* 1.3 60.4 + - - +
36H ILE* 3.4 26.1 + - + +
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Residues in contact with GLY 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 5.7 2.5 - - - -
147A SER* 4.7 10.3 + - - -
148A GLY* 4.9 2.6 + - - -
31H GLN* 2.7 27.9 + - - -
32H ASP 4.7 0.4 + - - -
33H LYS 3.7 0.6 - - - -
34H GLU* 1.3 72.1 - - - +
36H ILE* 1.3 59.7 + - - +
37H PRO* 3.1 13.2 - - - +
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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