Contacts of the helix formed by residues 20 - 36 (chain A) 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 SER 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE 2.8 13.2 + - - -
19A LYS* 1.3 86.4 - - - +
21A ALA* 1.3 62.3 + - - +
22A ASP 3.2 3.1 - - - -
23A ALA* 3.1 14.8 + - - +
24A ILE* 2.9 24.1 + - - +
113A MET* 5.2 3.1 - - - -
114A PHE* 3.6 27.7 - - - -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 3.7 25.1 - - + -
17A ILE 3.8 0.4 + - - -
18A GLY 3.1 18.3 + - - +
19A LYS 3.4 1.4 + - - -
20A SER* 1.3 75.6 - - - +
22A ASP* 1.3 67.4 + - - +
24A ILE* 3.2 11.0 + - - +
25A GLY 2.9 19.6 + - - -
64A MET* 3.1 25.1 - - + +
65A GLY* 6.1 0.4 - - - -
68A ALA* 6.0 0.2 - - + -
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Residues in contact with ASP 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LYS 5.1 1.0 + - - +
20A SER 3.2 0.8 - - - -
21A ALA* 1.3 80.6 - - - +
23A ALA* 1.3 63.9 + - - +
25A GLY* 3.3 1.0 + - - -
26A ASN* 3.1 23.2 + - - +
57A LYS* 6.0 0.2 - - - +
60A GLY 4.4 3.5 - - - -
61A LYS* 3.3 61.0 + - + +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A SER* 3.1 14.8 + - - +
22A ASP* 1.3 76.5 - - - +
24A ILE* 1.3 66.7 + - - +
26A ASN* 3.4 7.5 + - - +
27A ASP* 3.1 26.0 + - - +
113A MET* 3.8 17.7 - - + +
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 4.7 1.6 - - + -
17A ILE* 4.1 33.7 - - + +
20A SER* 2.9 26.0 + - - +
21A ALA* 3.2 10.1 + - - +
23A ALA* 1.3 78.0 - - - +
25A GLY* 1.3 57.7 + - - +
27A ASP* 3.3 1.7 + - - +
28A ALA* 2.9 28.1 + - + +
64A MET* 3.6 27.6 - - + -
106A ILE* 4.4 6.1 - - + -
109A VAL* 3.7 20.2 - - + +
110A ILE* 4.2 17.5 - - + -
113A MET* 3.8 18.4 - - - -
114A PHE* 4.2 9.0 - - + -
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 2.9 11.7 + - - -
22A ASP 3.8 0.2 - - - -
23A ALA 3.3 0.2 - - - -
24A ILE* 1.3 74.1 - - - +
26A ASN* 1.3 65.0 + - - +
28A ALA* 4.0 3.5 - - - +
29A LEU* 2.9 27.9 + - - +
60A GLY* 3.4 18.4 - - - -
63A VAL* 5.1 4.7 - - - +
64A MET* 3.3 22.4 - - - +
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Residues in contact with ASN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASP 3.1 16.4 + - - +
23A ALA* 3.8 7.1 + - - +
25A GLY* 1.3 75.5 - - - +
27A ASP* 1.3 62.3 + - - +
30A SER* 2.9 35.3 + - - -
51A PRO 4.3 10.0 + - - +
53A SER 4.6 0.7 - - - +
56A ILE* 3.4 16.2 - - - +
57A LYS* 3.2 43.6 + - + +
60A GLY* 3.7 8.8 - - - -
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Residues in contact with ASP 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA 3.1 16.0 + - - +
24A ILE 3.6 3.1 - - - +
26A ASN* 1.3 83.3 - - - +
28A ALA* 1.3 63.7 + - - +
30A SER* 3.4 7.3 + - - -
31A ARG* 2.9 56.6 + - - +
109A VAL* 3.6 17.5 - - + +
112A THR* 4.4 1.2 + - - -
113A MET* 3.0 22.6 - - + +
120B HIS* 4.0 10.6 + - - -
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE 2.9 18.3 + - - +
25A GLY* 4.0 5.2 - - - +
27A ASP* 1.3 75.2 - - - +
29A LEU* 1.3 58.0 + - - +
31A ARG* 3.5 0.9 + - - -
32A MET* 3.0 28.9 + - - +
63A VAL* 6.2 0.7 - - + -
102A LEU* 4.1 7.8 - - + +
105A CYS* 3.7 9.6 - - - +
106A ILE* 3.8 35.4 - - + +
109A VAL* 3.5 16.7 - - + +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLY 2.9 16.5 + - - +
26A ASN 3.8 3.1 - - - +
28A ALA* 1.3 75.1 - - - +
30A SER* 1.3 63.9 + - - +
32A MET* 3.4 28.2 + - + +
33A ILE* 3.1 28.5 + - + +
43A PHE* 4.0 16.6 - - + -
46A TRP* 4.3 3.6 - - + -
56A ILE* 3.4 42.6 - - + +
59A HIS* 3.7 31.6 - - + -
60A GLY* 3.9 4.7 - - - +
63A VAL* 4.5 9.9 - - + -
102A LEU* 4.5 7.8 - - + +
200A HEM 6.3 0.2 - - + -
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Residues in contact with SER 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ASN* 2.9 24.6 + - - -
27A ASP* 3.5 9.5 - - - -
28A ALA 3.3 0.2 - - - -
29A LEU* 1.3 76.9 - - - +
31A ARG* 1.3 63.5 + - - +
33A ILE* 3.5 4.2 + - - +
34A VAL* 3.2 29.7 + - - +
50A THR 5.7 0.2 - - - -
51A PRO* 3.5 42.8 + - - +
56A ILE* 3.5 11.4 - - - +
124B ALA* 4.9 1.8 - - - -
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Residues in contact with ARG 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASP* 2.9 34.8 + - - +
28A ALA 3.7 4.0 - - - +
30A SER* 1.3 74.6 - - - +
32A MET* 1.3 67.9 + - - +
35A VAL* 2.7 28.8 + - - +
105A CYS* 4.2 12.6 - - - -
108A VAL* 4.0 12.9 - - - +
109A VAL* 3.6 25.5 - - - +
112A THR* 4.4 11.7 + - - +
119B GLY 5.2 1.0 + - - -
120B HIS* 5.4 5.1 + - - -
122B PHE* 2.7 37.7 + - - -
123B THR* 3.5 15.0 + - - +
124B ALA* 4.0 18.8 - - + +
127B GLN* 3.0 34.2 + - - +
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Residues in contact with MET 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA 3.0 15.5 + - - +
29A LEU* 3.6 21.8 - - + +
30A SER 3.3 0.2 - - - -
31A ARG* 1.3 79.4 - - - +
33A ILE* 1.3 59.2 + - + +
36A TYR* 2.8 36.3 + - - +
39A THR* 3.5 21.8 - - + +
43A PHE* 3.9 20.9 - - + -
98A ASN 4.7 0.4 - - - +
101A ILE* 3.9 18.6 - - + -
102A LEU* 3.7 34.8 - - + -
105A CYS* 3.8 13.2 - - - -
200A HEM 3.9 30.1 - - + -
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.1 14.7 + - + +
30A SER* 4.0 4.7 - - - +
32A MET* 1.3 82.0 - - + +
34A VAL* 1.3 66.4 + - + +
37A PRO* 3.6 19.9 - - - +
39A THR* 3.5 14.8 - - - +
40A LYS* 3.8 36.3 + - + +
43A PHE* 3.3 34.3 - - + -
49A VAL* 3.2 39.9 - - + +
51A PRO* 6.5 0.2 - - + -
56A ILE* 3.9 15.5 - - + -
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A SER 3.2 18.9 + - - +
31A ARG 3.8 2.2 - - - +
33A ILE* 1.3 83.4 - - + +
35A VAL* 1.3 63.5 + - + +
36A TYR 3.6 0.2 + - - -
37A PRO* 4.0 8.7 - - - +
40A LYS* 6.0 0.4 - - - +
51A PRO* 3.8 27.8 - - + -
124B ALA* 3.8 30.5 - - + +
125B GLU* 4.5 6.3 - - + +
128B GLY* 6.1 0.7 - - - -
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG 2.7 23.8 + - - +
34A VAL* 1.3 75.5 - - + +
36A TYR* 1.3 83.4 + - + +
37A PRO* 3.3 8.6 - - - +
124B ALA* 3.4 27.8 - - - +
127B GLN* 4.0 14.6 - - - +
128B GLY* 3.6 24.0 - - - +
131B GLN* 3.5 22.4 - - + +
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Residues in contact with TYR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET* 2.8 24.2 + - - +
33A ILE 3.8 0.3 - - - +
35A VAL* 1.3 91.6 - - + +
37A PRO* 1.3 61.2 - - - +
38A GLN* 3.1 20.6 - - - +
39A THR* 2.8 33.6 + - + -
101A ILE* 3.3 45.5 - - + -
104A HIS* 3.3 20.9 - + - +
105A CYS* 3.7 21.5 - - - -
127B GLN* 4.7 1.1 - - - -
131B GLN* 2.9 27.3 + - - -
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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