Contacts of the helix formed by residues 19 - 35 (chain B) in PDB entry 2PEG
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 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B HIS 3.7 2.8 + - - +
18B MET* 1.3 73.2 - - - +
20B TYR* 1.3 57.9 + - - +
21B ASP* 3.1 22.8 + - - +
22B ASP* 3.0 22.3 + - + +
23B ILE* 2.9 33.3 + - + +
117B LYS* 5.2 2.0 - - - +
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Residues in contact with TYR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE* 3.4 41.6 + + - +
18B MET* 3.5 22.6 + - + -
19B ASP* 1.3 73.1 + - - +
21B ASP* 1.3 62.5 + - - +
24B GLY* 2.8 30.0 + - - -
25B PRO* 3.5 1.6 - - - +
65B ILE* 3.7 6.7 - - + +
68B LEU* 3.6 45.2 - - + +
69B HIS* 3.4 44.4 - + + +
72B ASP* 3.1 32.9 + - - -
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASP* 3.1 12.6 + - - +
20B TYR* 1.3 78.8 - - - +
22B ASP* 1.3 58.7 + - - +
25B PRO* 3.2 19.9 - - - +
65B ILE* 3.5 35.0 - - + +
69B HIS* 5.2 1.7 + - - -
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Residues in contact with ASP 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASP* 3.0 27.5 + - + +
21B ASP* 1.3 80.4 - - - +
23B ILE* 1.3 78.7 + - - +
25B PRO* 3.6 3.3 - - - +
26B LYS* 3.0 56.9 + - - +
117B LYS* 5.7 2.3 - - - +
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Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 3.6 31.2 - - + -
19B ASP* 2.9 22.6 + - + +
22B ASP* 1.3 88.7 - - - +
24B GLY* 1.3 58.0 + - - +
26B LYS* 3.3 2.0 + - + +
27B ALA* 2.9 31.7 + - + +
68B LEU* 3.9 17.9 - - + -
110B ILE* 5.0 7.2 - - + -
113B VAL* 3.8 29.3 - - + +
114B LEU* 4.7 5.6 - - - +
117B LYS* 4.0 30.5 - - + -
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B TYR 2.8 15.9 + - - -
23B ILE* 1.3 73.4 - - - +
25B PRO* 1.3 66.7 - - - +
27B ALA* 3.8 2.8 - - - +
28B LEU 3.2 18.0 + - - -
64B GLY* 3.3 35.2 - - - -
68B LEU* 3.2 17.4 - - - +
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Residues in contact with PRO 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR 3.5 4.3 - - - +
21B ASP 3.2 26.7 - - - +
22B ASP 3.6 4.9 - - - +
24B GLY* 1.3 89.8 - - - +
26B LYS* 1.3 55.4 + - + +
28B LEU* 4.1 1.5 - - + +
29B SER* 2.9 38.6 + - - +
55B ILE 5.6 4.7 - - - +
60B VAL* 4.6 0.4 - - - +
61B ALA* 3.6 46.4 - - + +
64B GLY* 4.6 1.6 - - - -
65B ILE* 3.6 10.5 - - + -
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PRO* 5.6 0.5 - - - +
22B ASP* 3.0 49.4 + - - +
23B ILE 3.3 4.4 + - - +
24B GLY 3.2 0.6 - - - -
25B PRO* 1.3 80.5 - - + +
27B ALA* 1.3 57.3 + - - +
29B SER* 4.0 3.3 - - - -
30B ARG* 2.9 32.2 + - - +
55B ILE* 6.5 1.1 - - + -
113B VAL* 3.8 22.8 - - + +
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ILE* 2.9 19.0 + - + +
24B GLY* 3.8 5.2 - - - +
26B LYS* 1.3 76.0 - - - +
28B LEU* 1.3 57.9 + - - +
30B ARG* 3.4 0.9 + - - +
31B CYS* 2.9 27.9 + - - +
68B LEU* 5.5 2.0 - - + -
106B LEU* 4.2 4.3 - - + -
109B CYS* 3.5 9.5 - - - +
110B ILE* 3.8 41.3 - - + -
113B VAL* 3.8 13.6 - - + +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY 3.2 14.4 + - - +
25B PRO 4.1 2.0 - - - +
27B ALA* 1.3 76.5 - - - +
29B SER* 1.3 61.1 + - - +
31B CYS* 3.2 6.0 + - + +
32B LEU* 2.9 49.1 + - + +
42B PHE* 3.8 22.9 - - + -
60B VAL* 3.1 37.0 - - + +
63B HIS* 3.3 30.5 - - + +
64B GLY* 3.7 9.0 - - - +
67B VAL* 5.5 0.7 - - + -
106B LEU* 4.1 25.0 - - + +
400B HEM 5.6 3.8 - - + -
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Residues in contact with SER 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PRO* 5.2 1.1 - - - -
25B PRO* 2.9 25.9 + - - +
26B LYS* 4.1 4.0 - - - -
28B LEU* 1.3 73.3 - - - +
30B ARG* 1.3 62.5 + - - +
32B LEU* 3.2 2.3 + - - +
33B ILE* 3.1 29.3 + - - +
54B ILE* 3.5 27.9 + - - -
55B ILE* 3.6 26.8 + - - +
60B VAL* 3.4 16.3 - - - +
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Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 5.6 1.3 + - - -
115A PRO 5.4 1.8 + - - -
118A PHE* 2.9 36.9 + - - -
119A THR* 3.5 2.2 + - - +
120A PRO* 3.5 36.0 - - + +
123A HIS* 2.9 51.0 + - - +
26B LYS 2.9 18.7 + - - +
27B ALA* 3.6 5.4 - - - +
29B SER* 1.3 77.9 - - - +
31B CYS* 1.3 56.4 + - - +
33B ILE* 3.2 2.3 + - - +
34B VAL* 2.9 39.5 + - + +
109B CYS* 4.1 10.5 - - - -
112B ILE* 4.1 11.6 - - - +
113B VAL* 3.7 23.8 - - + +
116B ALA* 6.0 3.4 - - - +
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Residues in contact with CYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA 2.9 14.7 + - - +
28B LEU* 3.4 10.3 - - + +
30B ARG* 1.3 76.6 - - - +
32B LEU* 1.3 59.4 + - + +
35B TYR* 2.9 41.3 + - - +
38B THR* 3.9 24.2 - - - -
102B ASN 5.0 0.9 - - - -
105B LEU* 4.4 1.1 - - - -
106B LEU* 3.8 42.6 - - + -
109B CYS* 3.5 13.4 - - - -
400B HEM 5.6 2.0 - - - -
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 2.9 37.4 + - + +
29B SER 3.2 4.9 + - - +
31B CYS* 1.3 78.1 - - + +
33B ILE* 1.3 58.0 + - - +
36B PRO* 3.0 13.2 - - - +
38B THR* 3.3 28.0 - - - +
39B GLN* 2.8 49.7 + - + +
42B PHE* 4.0 17.0 - - + -
54B ILE* 3.9 17.5 - - + -
60B VAL* 3.6 32.8 - - + -
400B HEM 5.6 0.2 - - + -
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Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PRO* 3.7 37.9 - - + +
121A GLU* 3.7 28.5 - - + +
124A VAL* 3.5 17.8 - - + +
29B SER 3.1 19.3 + - - +
30B ARG 3.8 2.5 - - - +
32B LEU* 1.3 78.0 - - - +
34B VAL* 1.3 64.4 + - - +
35B TYR 3.4 0.2 - - - -
36B PRO* 3.6 10.7 - - - +
39B GLN* 4.6 2.7 - - - +
51B ALA* 3.9 18.4 - - + +
54B ILE* 4.0 18.4 - - + -
55B ILE* 3.9 20.4 - - + -
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PRO* 3.9 14.4 - - + +
123A HIS* 3.5 49.8 - - + +
124A VAL* 3.6 22.9 - - - +
127A ASP* 4.2 9.1 - - + +
30B ARG* 2.9 24.5 + - + +
33B ILE* 1.3 79.3 - - - +
35B TYR* 1.3 93.2 + - + +
36B PRO* 3.4 6.7 - - - +
37B TRP* 4.7 2.8 - - - -
109B CYS* 4.7 0.7 - - - -
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 6.2 0.2 - - - +
123A HIS* 5.2 2.8 + - - -
127A ASP* 3.9 21.0 + - - -
31B CYS* 2.9 18.1 + - - +
34B VAL* 1.3 103.1 - - + +
36B PRO* 1.3 66.5 - - - +
37B TRP* 2.9 41.7 + + + +
38B THR* 2.8 26.8 + - + +
105B LEU* 3.6 56.4 - - + +
108B ASP* 4.7 13.7 + - + +
109B CYS* 3.9 13.9 - - - -
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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