Contacts of the helix formed by residues 22 - 34 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLY* 3.3 27.1 - - - -
26A SER* 3.8 0.2 - - - -
321A ILE* 5.5 0.2 - - - -
18B HIS 3.3 2.3 + - - -
19B HIS 3.1 9.4 + - - -
20B PHE 3.2 1.2 - - - -
21B LEU* 1.3 77.6 - - - +
23B TYR* 1.3 61.6 + - - +
25B ASN* 3.0 18.4 + - - +
26B SER 3.5 0.7 + - - -
404B GOL 3.2 31.9 - - - -
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Residues in contact with TYR 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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23A TYR* 3.7 30.0 - - + +
26A SER* 3.1 26.0 + - - +
27A MET* 6.3 2.2 - - + -
122A SER 2.7 30.7 + - - -
123A VAL* 4.2 2.2 - - + -
127A LEU* 3.9 7.8 + - - +
128A VAL* 3.8 42.4 - - + -
131A TRP* 4.1 7.4 - + - -
325A LEU* 3.9 20.4 - - - +
20B PHE 3.5 12.3 - - - -
21B LEU* 3.0 12.1 + - + +
22B GLY* 1.3 76.2 - - - +
24B ILE* 1.3 78.0 + - + +
26B SER* 3.3 3.9 + - - -
27B MET* 3.0 42.4 + - + +
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Residues in contact with ILE 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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131A TRP* 3.5 32.8 - - + +
321A ILE* 3.9 15.9 - - + +
324A MET* 3.6 26.7 - - + -
325A LEU* 4.1 17.9 - - + -
21B LEU* 2.8 31.6 + - + +
23B TYR* 1.3 95.9 - - + +
25B ASN* 1.3 58.9 + - - +
27B MET* 4.1 2.4 - - - +
28B THR* 2.8 42.7 + - + +
73B MET* 4.2 9.9 - - + -
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Residues in contact with ASN 25 (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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19A HIS* 3.4 13.5 - - + +
321A ILE* 3.8 8.0 - - - +
22B GLY 3.0 6.4 + - - +
24B ILE* 1.3 74.6 - - - +
26B SER* 1.3 66.0 + - - +
28B THR* 3.0 16.4 + - - -
29B LEU* 3.0 16.5 + - - +
73B MET* 3.0 26.2 - - - +
77B LEU* 3.8 8.5 - - + +
402B GOL 2.9 33.3 + - - -
404B GOL 2.7 43.9 + - - +
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Residues in contact with SER 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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19A HIS 3.3 6.4 + - - -
20A PHE* 2.8 30.1 + - - +
22A GLY 3.3 3.5 + - - -
23A TYR* 3.1 30.2 + - - -
22B GLY 3.5 0.6 + - - -
23B TYR* 3.3 11.1 + - - -
25B ASN* 1.3 79.8 - - - +
27B MET* 1.3 62.4 + - - +
29B LEU* 3.9 2.3 - - - +
30B GLN* 3.0 28.2 + - - +
119B THR* 5.3 0.2 - - - +
123B VAL* 3.8 16.8 - - - +
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Residues in contact with MET 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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23A TYR* 6.3 1.8 - - + -
128A VAL* 4.1 23.6 - - + +
131A TRP* 3.4 47.3 - - + +
132A ARG* 3.8 39.5 - - + +
23B TYR* 3.0 30.5 + - + +
24B ILE* 4.1 1.6 - - - +
26B SER* 1.3 79.4 - - - +
28B THR* 1.3 61.5 + - - +
30B GLN* 3.4 23.8 + - - +
31B CYS* 3.0 32.4 + - - -
123B VAL* 4.8 7.4 - - + +
128B VAL* 5.5 4.5 - - + -
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Residues in contact with THR 28 (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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131A TRP* 3.7 28.9 - - + -
324A MET* 3.8 18.8 - - + -
24B ILE* 2.8 36.2 + - + +
25B ASN* 3.0 14.0 + - - -
27B MET* 1.3 73.1 - - - +
29B LEU* 1.3 62.6 + - - +
31B CYS* 3.3 4.8 + - - +
32B ALA* 3.1 21.1 + - - +
70B LEU* 4.3 13.5 - - + +
73B MET* 4.0 15.4 - - + +
74B LEU* 4.1 8.0 - - - +
77B LEU* 4.2 5.9 - - - +
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Residues in contact with LEU 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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16A VAL* 4.2 12.1 - - + -
19A HIS* 4.0 12.3 - - + -
20A PHE* 3.9 25.4 - - + +
25B ASN 3.0 17.6 + - - +
26B SER* 3.9 3.4 - - - +
28B THR* 1.3 78.4 + - - +
30B GLN* 1.3 63.2 + - - +
32B ALA* 3.1 11.5 + - + +
33B LEU* 3.1 28.2 + - + +
74B LEU* 4.6 4.9 - - + +
77B LEU* 5.4 2.0 - - + -
79B TYR* 3.6 42.0 - - + +
107B LEU* 4.1 24.2 - - + -
119B THR* 4.3 11.4 - - + +
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Residues in contact with GLN 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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131A TRP 5.1 1.8 + - - -
132A ARG* 4.0 21.2 + - - +
26B SER 3.0 17.9 + - - +
27B MET* 3.7 23.7 + - - +
28B THR 3.3 0.4 - - - -
29B LEU* 1.3 76.0 - - - +
31B CYS* 1.3 57.8 + - - +
33B LEU* 3.1 8.6 + - - +
34B GLU* 2.8 52.3 + - + +
119B THR* 4.6 6.7 - - + +
120B PHE* 3.6 20.6 - - + +
123B VAL* 3.1 33.7 - - + +
124B HIS* 5.8 0.3 - - - -
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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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131A TRP* 4.2 13.7 - - - -
134A MET* 3.6 38.1 - - + -
135A SER* 3.6 18.6 - - - +
138A LEU* 5.5 0.2 - - + -
27B MET 3.0 18.9 + - - +
28B THR* 3.5 9.9 - - - +
30B GLN* 1.3 76.5 - - - +
32B ALA* 1.3 59.2 + - - +
34B GLU* 3.1 5.5 + - - +
35B LEU* 2.8 38.9 + - + +
70B LEU* 4.6 15.3 - - + -
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Residues in contact with ALA 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 THR 3.1 10.7 + - - +
29B LEU* 3.4 15.7 - - + +
31B CYS* 1.3 78.0 - - - +
33B LEU* 1.3 64.5 + - + +
36B ASP* 3.2 2.3 + - - -
37B ILE* 3.1 47.5 + - + +
38B ALA 4.8 0.9 + - - -
70B LEU* 5.1 0.8 - - - +
74B LEU* 3.9 28.7 - - + -
80B PHE* 5.1 4.9 - - + -
107B LEU* 5.2 4.3 - - + -
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Residues in contact with LEU 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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29B LEU* 3.1 17.5 + - + +
30B GLN 3.6 5.8 - - - +
31B CYS 3.1 0.2 - - - -
32B ALA* 1.3 77.7 - - - +
34B GLU* 1.3 65.1 + - - +
36B ASP* 2.9 14.4 + - - +
107B LEU* 3.9 38.1 - - + +
116B ARG* 3.0 55.1 + - + +
119B THR* 3.5 42.6 - - + +
120B PHE* 3.6 17.9 - - + -
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Residues in contact with GLU 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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131A TRP 5.2 2.1 - - - +
132A ARG* 4.7 11.9 - - - +
135A SER* 2.7 40.8 + - - +
139A ARG* 4.1 12.3 + - - +
30B GLN* 2.8 40.1 + - - +
31B CYS* 3.6 9.2 - - - +
33B LEU* 1.3 76.3 - - - +
35B LEU* 1.3 60.7 + - - +
36B ASP* 3.5 5.0 + - - +
116B ARG* 5.5 0.2 - - - +
120B PHE* 3.9 19.4 - - + -
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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