Contacts of the helix formed by residues 22 - 34 (chain A) in PDB entry 4EVI
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A HIS 3.2 1.6 + - - -
19A HIS 3.1 9.0 + - - -
20A PHE 3.2 1.2 - - - -
21A LEU* 1.3 78.1 - - - +
23A TYR* 1.3 56.0 + - - +
25A ASN* 2.9 29.8 + - - +
26A SER 3.6 0.3 + - - -
22B GLY* 3.3 28.8 - - - -
26B SER* 3.3 0.2 + - - -
404B GOL 3.4 25.4 - - - -
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Residues in contact with TYR 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 PHE 3.5 14.4 - - - -
21A LEU* 3.1 11.0 + - + +
22A GLY* 1.3 74.3 - - - +
24A ILE* 1.3 78.7 + - + +
25A ASN 3.3 0.2 - - - -
26A SER* 3.2 4.9 + - - -
27A MET* 2.9 43.3 + - + +
22B GLY 3.8 0.6 + - - -
23B TYR* 3.7 29.8 - - + +
26B SER* 3.1 21.4 + - - +
27B MET* 6.3 1.8 - - + -
122B SER 2.7 30.4 + - - -
123B VAL* 4.3 2.0 - - + -
127B LEU* 4.0 6.9 + - - +
128B VAL* 3.7 43.7 - - + -
131B TRP* 4.0 6.5 - + - -
325B LEU* 3.9 21.3 - - - +
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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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21A LEU* 2.9 23.2 + - + +
23A TYR* 1.3 98.4 - - + +
25A ASN* 1.3 60.0 + - - +
27A MET* 4.5 2.5 - - - +
28A THR* 2.9 43.7 + - + +
73A MET* 4.3 6.1 - - + -
131B TRP* 3.3 33.9 - - + +
321B ILE* 4.1 21.8 - - + +
324B MET* 3.6 28.7 - - + -
325B LEU* 4.3 15.0 - - + -
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Residues in contact with ASN 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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18A HIS* 4.5 4.0 + - - -
21A LEU 4.1 0.2 + - - -
22A GLY 2.9 10.0 + - - +
24A ILE* 1.3 78.6 - - - +
26A SER* 1.3 61.8 + - - +
28A THR* 3.2 5.5 + - - -
29A LEU* 3.1 25.6 + - - +
73A MET* 3.1 25.5 - - - +
77A LEU* 3.7 18.2 - - + +
19B HIS* 3.4 28.7 - - + +
321B ILE* 3.7 13.8 - - - +
404B GOL 2.9 37.2 + - - +
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Residues in contact with SER 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 GLY 3.6 0.6 + - - -
23A TYR* 3.2 12.8 + - - -
25A ASN* 1.3 80.7 - - - +
27A MET* 1.3 62.4 + - - +
29A LEU* 3.9 2.1 - - - +
30A GLN* 3.0 27.9 + - - +
119A THR* 5.3 0.2 - - - +
123A VAL* 3.9 17.1 - - - +
19B HIS 3.4 5.8 + - - -
20B PHE* 2.7 30.2 + - - +
22B GLY 3.3 2.1 + - - -
23B TYR* 3.1 30.4 + - - -
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Residues in contact with MET 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 TYR* 2.9 28.7 + - + +
24A ILE* 4.1 2.2 - - - +
26A SER* 1.3 78.4 - - - +
28A THR* 1.3 62.7 + - - +
30A GLN* 3.9 22.7 + - - +
31A CYS* 2.9 33.1 + - - -
123A VAL* 4.8 7.9 - - + +
128A VAL* 5.5 4.0 - - + -
23B TYR* 6.3 2.2 - - + -
128B VAL* 4.2 20.2 - - + -
131B TRP* 3.4 50.6 - - + +
132B ARG* 3.9 37.0 - - + +
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Residues in contact with THR 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 38.7 + - + +
25A ASN* 3.2 9.7 + - - -
27A MET* 1.3 73.0 - - - +
29A LEU* 1.3 67.5 + - - +
31A CYS* 3.3 5.1 + - - +
32A ALA* 3.0 21.1 + - - +
70A LEU* 4.0 16.0 - - + +
73A MET* 4.0 9.1 - - + +
74A LEU* 4.0 7.8 - - - +
77A LEU* 3.9 13.5 - - - +
131B TRP* 3.9 20.9 - - + -
324B MET* 3.9 19.1 - - + -
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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 ASN 3.1 13.5 + - - +
26A SER 3.9 2.7 - - - +
28A THR* 1.3 82.3 + - - +
30A GLN* 1.3 62.5 + - - +
32A ALA* 3.1 12.7 + - + +
33A LEU* 3.1 24.8 + - + +
74A LEU* 4.4 5.3 - - + +
77A LEU* 5.5 2.0 - - + -
79A TYR* 3.5 42.2 - - + +
107A LEU* 4.2 25.6 - - + -
119A THR* 4.4 10.1 - - + +
16B VAL* 3.9 17.5 - - + -
19B HIS* 4.0 15.3 - - + -
20B PHE* 4.1 17.3 - - + -
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Residues in contact with GLN 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 SER 3.0 18.8 + - - +
27A MET* 3.4 24.1 + - - +
28A THR 3.3 0.2 - - - -
29A LEU* 1.3 75.4 - - - +
31A CYS* 1.3 59.6 + - - +
33A LEU* 3.1 8.3 + - - +
34A GLU* 2.8 53.1 + - + +
119A THR* 4.7 6.4 - - + +
120A PHE* 3.6 23.1 - - + +
123A VAL* 3.0 32.6 - - + +
124A HIS* 5.7 0.5 - - - -
131B TRP 5.2 1.6 + - - -
132B ARG* 4.2 20.4 + - - +
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Residues in contact with CYS 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 MET 2.9 21.1 + - - -
28A THR* 3.4 10.5 - - - +
29A LEU 3.2 0.2 - - - -
30A GLN* 1.3 76.8 - - - +
32A ALA* 1.3 57.5 + - - +
34A GLU* 3.1 8.0 + - - +
35A LEU* 2.8 37.8 + - + +
70A LEU* 4.5 15.3 - - + -
131B TRP* 4.3 13.5 - - - -
134B MET* 3.6 37.7 - - - -
135B SER* 3.6 19.7 - - - +
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Residues in contact with ALA 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 THR 3.0 9.7 + - - +
29A LEU* 3.1 16.6 + - + +
31A CYS* 1.3 75.7 - - - +
33A LEU* 1.3 60.2 + - + +
36A ASP 3.2 4.9 + - - -
37A ILE* 3.1 44.7 + - + +
38A ALA 4.8 0.7 + - - -
70A LEU* 5.1 0.6 - - - +
74A LEU* 3.7 32.9 - - + +
80A PHE* 4.7 9.2 - - + -
107A LEU* 5.3 2.5 - - + -
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Residues in contact with LEU 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 16.2 + - + +
30A GLN* 3.5 5.8 - - - +
32A ALA* 1.3 77.5 - - - +
34A GLU* 1.3 65.2 + - - +
35A LEU 3.2 0.2 - - - -
36A ASP* 3.0 10.7 + - - +
38A ALA* 6.3 0.4 - - + -
107A LEU* 3.8 39.0 - - + +
116A ARG* 3.0 57.5 + - + +
119A THR* 3.4 41.7 - - + +
120A PHE* 3.6 19.1 - - + -
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Residues in contact with GLU 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 GLN* 2.8 49.1 + - + +
31A CYS* 3.5 9.2 - - - +
33A LEU* 1.3 73.6 - - - +
35A LEU* 1.3 61.5 + - - +
36A ASP* 3.4 3.1 + - - +
120A PHE* 4.1 13.1 - - + -
131B TRP 5.2 2.4 - - - +
132B ARG* 4.8 11.3 - - - +
135B SER* 2.7 43.1 + - - +
139B ARG* 4.3 11.4 + - - -
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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