Contacts of the strand formed by residues 27 - 41 (chain H) in PDB entry 2PGW
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 GLY 27 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H HIS* 3.9 0.3 - - - +
24H TRP* 3.1 31.8 + - - +
25H SER 3.7 2.4 + - - -
26H TYR* 1.3 73.9 - - - +
28H ILE* 1.3 73.9 + - - +
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Residues in contact with ILE 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H PRO* 3.2 35.9 - - + -
22H TYR 3.6 8.1 - - - +
23H HIS* 3.4 33.9 - - + +
24H TRP* 3.6 8.4 + - - -
26H TYR 4.9 0.5 - - - +
27H GLY* 1.3 83.7 - - - +
29H ARG* 1.3 67.0 + - - +
30H GLU* 4.2 8.3 + - + +
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Residues in contact with ARG 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C GLY 3.2 19.8 + - - -
94C HIS* 3.6 26.1 + - - -
18H LEU* 3.8 5.0 - - + +
21H PRO* 3.5 1.7 - - - +
22H TYR* 2.7 59.5 + - + +
24H TRP* 3.3 37.6 - - + +
28H ILE* 1.3 74.3 - - - +
30H GLU* 1.3 60.8 + - - +
31H SER 3.4 21.5 - - - +
32H PHE* 3.9 20.6 - - - -
301H PHE* 3.1 41.2 - - - -
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Residues in contact with GLU 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H PRO* 3.6 4.3 - - - +
18H LEU* 2.9 29.0 + - - +
20H GLN 5.6 0.4 - - - -
21H PRO* 4.6 23.3 - - + +
28H ILE* 4.7 7.6 - - + -
29H ARG* 1.3 77.3 - - - +
31H SER* 1.3 63.4 + - - +
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Residues in contact with SER 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H VAL* 3.8 19.0 - - - +
16H LEU 3.1 24.7 - - - -
17H PRO* 3.8 4.7 - - - -
18H LEU* 3.7 5.0 - - - +
29H ARG* 3.4 20.6 - - - +
30H GLU* 1.3 80.8 + - - +
32H PHE* 1.3 67.0 + - - +
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Residues in contact with PHE 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H VAL* 3.6 2.5 - - - +
16H LEU* 2.8 41.3 + - + +
18H LEU* 3.4 37.4 - - + +
22H TYR* 4.8 4.7 - + - -
29H ARG* 3.9 15.5 - - - -
31H SER* 1.3 81.4 - - - +
33H ALA* 1.3 60.8 + - - +
34H VAL* 5.4 2.2 - - + -
301H PHE* 3.4 67.3 - + + +
302H THR* 3.9 15.5 - - - +
303H THR* 6.4 0.2 - - + -
327H MSE 4.6 4.3 - - + -
330H LEU* 4.0 28.3 - - + -
331H VAL* 4.3 7.2 - - + -
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Residues in contact with ALA 33 (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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14H LEU 3.2 13.5 - - - +
15H VAL* 4.6 6.7 - - + -
32H PHE* 1.3 77.4 - - - +
34H VAL* 1.3 68.6 + - - +
52H THR* 4.7 1.7 - - - -
53H VAL* 3.7 27.9 + - + +
57H GLN* 3.6 20.9 - - + +
301H PHE 4.4 5.1 + - - +
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Residues in contact with VAL 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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12H ARG 3.9 0.2 - - - +
14H LEU* 2.8 56.0 + - + +
16H LEU* 4.4 3.8 - - + -
32H PHE* 5.4 2.2 - - + -
33H ALA* 1.3 80.8 - - - +
35H ASN* 1.3 62.5 + - - +
36H LEU* 4.3 3.8 - - + -
50H GLU* 3.9 22.0 - - + +
51H CYS 3.5 9.9 - - - +
52H THR* 5.3 0.2 - - - -
53H VAL* 3.8 1.3 - - - -
57H GLN* 3.1 2.8 + - - -
301H PHE 4.2 1.6 - - - +
302H THR* 3.8 41.3 - - + -
303H THR* 3.9 15.3 - - + -
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Residues in contact with ASN 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H VAL* 4.5 2.5 - - + -
12H ARG 3.9 2.2 - - - -
13H PRO* 3.3 16.5 - - - +
34H VAL* 1.3 71.4 + - - +
36H LEU* 1.3 65.6 + - - +
37H ILE 3.7 0.2 + - - -
50H GLU* 3.3 2.5 - - - -
51H CYS* 3.0 33.9 + - + +
52H THR 4.8 0.9 - - - +
53H VAL* 3.4 9.0 - - - +
57H GLN* 3.1 39.1 - - - +
60H THR* 3.3 23.7 + - - -
61H ALA* 3.4 15.1 + - - +
64H LEU* 3.7 22.6 - - + +
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Residues in contact with LEU 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ARG 4.3 0.2 - - - -
11H VAL* 3.2 9.4 - - - +
12H ARG* 3.0 53.0 + - + +
14H LEU* 3.6 33.4 - - + -
34H VAL* 4.3 2.0 - - + -
35H ASN* 1.3 74.0 - - - +
37H ILE* 1.3 62.0 + - - +
38H GLU* 4.2 6.7 - - + +
48H ILE* 5.1 2.7 - - + -
49H GLY 3.4 4.3 - - - +
50H GLU* 3.7 18.2 - - + +
64H LEU* 4.1 0.6 - - - +
305H ILE* 3.4 31.0 - - + -
335H ILE* 4.1 7.0 - - + -
360H LEU* 4.6 11.4 - - + -
365H VAL* 4.0 18.2 - - + -
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Residues in contact with ILE 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 4.4 4.5 - - + -
10H ARG 3.4 9.0 - - - +
11H VAL* 4.2 9.9 - - + -
35H ASN 4.7 1.1 - - - +
36H LEU* 1.3 75.1 - - - +
38H GLU* 1.3 71.9 + - - +
39H ILE* 4.1 19.1 - - + -
47H GLY 3.7 1.0 - - - +
48H ILE* 3.6 3.1 - - - -
49H GLY* 2.9 34.7 + - - +
50H GLU* 3.9 2.9 - - - +
64H LEU* 4.1 19.3 - - + -
68H ALA* 3.6 31.2 - - + -
108H GLY* 3.4 32.1 - - - +
109H ILE* 4.1 5.4 - - + +
112H ALA* 4.0 2.1 - - + +
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Residues in contact with GLU 38 (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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8H ASN 3.8 0.3 - - - +
9H VAL* 3.1 7.4 - - - +
10H ARG* 2.6 83.4 + - + +
12H ARG* 2.7 47.7 + - - -
36H LEU* 4.7 6.7 - - + +
37H ILE* 1.3 79.0 - - - +
39H ILE* 1.3 62.0 + - - +
40H GLU 4.1 0.7 - - - -
46H VAL* 4.1 6.5 - - + -
47H GLY 3.4 3.8 - - - -
48H ILE* 4.2 25.8 - - + +
360H LEU* 5.0 2.3 - - - +
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Residues in contact with ILE 39 (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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6H ILE* 3.5 41.1 - - + -
8H ASN 3.5 3.1 - - - +
9H VAL* 4.5 7.4 - - + -
37H ILE* 4.1 15.0 - - + -
38H GLU* 1.3 76.5 - - - +
40H GLU* 1.3 58.7 + - - +
45H THR 3.9 0.5 - - - +
46H VAL* 3.3 3.4 - - - -
47H GLY* 2.8 38.9 + - - +
71H LEU* 3.9 12.6 - - + -
109H ILE* 3.9 3.8 - - + +
112H ALA* 3.5 27.1 - - + -
113H MSE 3.7 27.4 - - + +
116H LEU* 3.9 17.5 - - + +
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Residues in contact with GLU 40 (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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6H ILE* 3.6 3.9 - - - -
7H SER* 2.7 36.6 + - - +
8H ASN* 2.8 40.8 + - + +
10H ARG* 2.6 37.6 + - - +
38H GLU 4.1 0.4 - - - -
39H ILE* 1.3 75.8 - - - +
41H ALA* 1.3 63.6 + - - +
44H GLY* 3.9 17.8 - - - +
45H THR 3.4 9.6 - - - +
46H VAL* 3.8 11.7 - - + -
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Residues in contact with ALA 41 (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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4H VAL* 3.5 19.7 - - + -
5H LYS 3.4 7.4 - - - +
6H ILE* 4.2 2.7 - - - +
7H SER* 3.0 12.6 + - - -
39H ILE 4.1 1.0 + - - -
40H GLU* 1.3 75.1 - - - +
42H ASP* 1.3 59.3 + - - +
43H ASP* 3.0 20.2 - - - +
44H GLY 2.9 17.5 + - - -
45H THR* 2.8 12.9 + - - +
76H PRO* 5.7 0.9 - - + -
116H LEU* 4.2 20.1 - - + +
120H LEU* 4.7 2.5 - - + -
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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