Contacts of the helix formed by residues 14 - 32 (chain A) in PDB entry 5IWM
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 ILE 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ARG 3.4 1.6 + - - -
13A ASN* 1.3 78.0 + - - +
15A THR* 1.3 64.7 + - - +
17A GLU* 3.5 5.5 + - - +
18A MET* 3.0 31.5 + - + +
521B LEU* 4.4 16.2 - - + -
525B TYR* 4.1 4.9 - - + -
532B ILE* 3.8 30.3 - - + -
606B VAL* 3.7 21.5 - - + -
607B LYS 2.8 19.0 + - - +
608B LEU* 4.0 25.6 - - + -
609B GLU 5.3 0.2 - - - +
614B ALA* 4.6 5.8 - - + -
618B PHE* 3.7 30.7 - - + -
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Residues in contact with THR 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN* 2.7 18.7 + - - -
14A ILE* 1.3 75.6 - - - +
16A SER* 1.3 62.2 + - - +
18A MET* 3.3 6.5 + - - +
19A ARG* 3.1 41.1 + - - +
610B ASP 4.8 1.9 + - - -
613B GLU* 4.1 23.3 + - - +
614B ALA* 3.7 28.1 + - - +
617B THR* 3.4 26.0 - - - +
618B PHE* 6.1 0.9 - - - -
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Residues in contact with SER 16 (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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12A ARG* 4.0 11.7 - - - -
13A ASN* 3.2 26.4 + - - +
15A THR* 1.3 77.1 - - - +
17A GLU* 1.3 64.8 + - - +
19A ARG* 3.6 6.8 + - - +
20A GLU* 3.1 43.2 + - - +
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Residues in contact with GLU 17 (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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12A ARG* 2.9 38.8 + - + +
13A ASN 2.9 16.0 + - - +
14A ILE* 3.6 7.9 - - - +
16A SER* 1.3 75.9 - - - +
18A MET* 1.3 61.8 + - - +
21A SER* 2.6 50.6 + - - -
517B ARG* 2.7 25.5 + - - +
521B LEU* 3.8 22.7 - - + -
539B ILE* 3.9 17.2 - - + +
604B LEU* 5.5 2.3 - - - +
606B VAL* 6.1 1.1 - - + -
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Residues in contact with MET 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.0 21.6 + - + +
15A THR* 3.8 4.7 - - - +
16A SER 3.3 0.2 - - - -
17A GLU* 1.3 77.4 - - - +
19A ARG* 1.3 56.8 + - - +
22A PHE* 3.0 34.1 + - - +
518B THR* 3.8 27.0 - - + +
521B LEU* 3.8 24.2 - - + -
522B THR* 3.8 12.1 - - - +
617B THR* 4.3 7.2 - - + -
618B PHE* 3.6 42.8 - - + -
621B LEU* 3.9 16.4 - - + -
622B MET* 3.8 24.9 - - + -
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Residues in contact with ARG 19 (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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15A THR* 3.1 33.4 + - - +
16A SER* 4.0 6.1 - - - +
18A MET* 1.3 74.4 - - - +
20A GLU* 1.3 62.3 + - + +
23A LEU* 3.2 31.4 + - - +
613B GLU* 4.5 13.6 + - - +
617B THR* 3.4 28.4 + - + -
620B MET* 4.2 13.1 - - + +
621B LEU* 4.1 7.4 - - + -
632B PHE* 3.7 41.4 - - + -
636B ASN* 4.9 3.6 - - - +
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Residues in contact with GLU 20 (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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12A ARG* 2.6 41.9 + - - +
16A SER* 3.1 22.1 + - - +
19A ARG* 1.3 82.7 - - + +
21A SER* 1.3 64.1 + - - +
23A LEU* 4.2 4.5 - - - +
24A ASP* 3.1 25.1 + - - +
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Residues in contact with SER 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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12A ARG* 5.3 0.4 + - - +
17A GLU* 2.6 40.2 + - - -
20A GLU* 1.3 76.5 - - - +
22A PHE* 1.3 62.5 + - - +
24A ASP* 3.4 5.3 + - - +
25A TYR* 3.1 21.8 + - - +
514B ALA* 4.0 18.5 - - - +
517B ARG* 3.3 12.9 + - - -
518B THR* 3.7 19.9 - - - +
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Residues in contact with PHE 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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18A MET* 3.0 23.2 + - + +
19A ARG 4.3 1.1 - - - +
21A SER* 1.3 75.0 - - - +
23A LEU* 1.3 60.6 + - - +
25A TYR* 3.3 7.4 + + - +
26A ALA* 2.9 28.2 + - + +
177A VAL* 3.9 19.7 - - + -
515B HIS* 4.1 20.0 - + - -
518B THR* 4.0 15.8 - - + +
621B LEU* 3.5 39.9 - - + -
622B MET* 3.6 33.0 - - + -
629B ARG* 3.8 28.5 - - + -
632B PHE* 5.1 3.4 - + - -
633B ILE* 5.7 1.6 - - + -
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Residues in contact with LEU 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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19A ARG 3.2 19.1 + - - +
20A GLU* 4.2 4.5 - - - +
22A PHE* 1.3 74.6 - - - +
24A ASP* 1.3 60.4 + - - +
26A ALA* 4.3 3.4 - - + -
27A MET* 2.9 49.9 + - + +
632B PHE* 3.6 25.7 - - + -
633B ILE* 3.9 32.8 - - + +
636B ASN* 3.4 31.9 - - + +
637B ALA* 4.3 6.3 - - - +
638B VAL 5.4 0.4 - - - +
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Residues in contact with ASP 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU 3.1 20.3 + - - +
21A SER* 3.5 6.5 - - - +
23A LEU* 1.3 78.8 - - - +
25A TYR* 1.3 61.6 + - - +
27A MET* 3.9 4.0 - - - +
28A SER* 3.2 22.2 + - - -
510B ASP 5.7 0.3 - - - -
511B VAL* 3.7 21.9 - - - +
514B ALA* 4.4 12.0 - - - +
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Residues in contact with TYR 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 SER 3.1 11.6 + - - +
22A PHE* 3.3 13.0 + + - +
24A ASP* 1.3 80.8 - - - +
26A ALA* 1.3 62.9 + - + +
28A SER* 3.3 3.8 + - - -
29A VAL* 3.1 43.5 + - + +
33A ARG* 4.0 7.0 + - - -
177A VAL* 3.8 25.4 - - + +
460B LYS* 3.4 13.7 + - - -
511B VAL* 3.2 36.1 - - + +
512B ASP* 3.3 21.3 - - - -
515B HIS* 3.5 50.0 + + + -
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Residues in contact with ALA 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 PHE* 2.9 21.5 + - + +
23A LEU* 4.0 6.7 - - + +
25A TYR* 1.3 79.2 - - - +
27A MET* 1.3 62.2 + - - +
29A VAL* 3.4 2.1 + - - +
30A ILE* 3.0 31.5 + - + +
177A VAL* 3.8 35.6 - - + +
633B ILE* 4.1 19.5 - - + -
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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
----------------------------------------------------------
23A LEU* 2.9 41.1 + - + +
24A ASP* 3.9 5.6 - - - +
26A ALA* 1.3 76.2 - - - +
28A SER* 1.3 58.0 + - - +
30A ILE* 3.5 5.5 + - - +
31A VAL* 3.0 41.2 + - + +
633B ILE* 5.0 4.7 - - + -
637B ALA* 3.3 27.1 - - - -
638B VAL 3.6 22.7 - - - +
639B TYR* 3.6 38.4 - - + -
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Residues in contact with SER 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 ASP* 3.2 16.6 + - - -
25A TYR 3.6 4.3 - - - -
27A MET* 1.3 76.8 - - - +
29A VAL* 1.3 58.5 + - - +
31A VAL* 4.5 5.4 - - - -
32A ALA* 2.7 45.2 + - - +
33A ARG* 5.0 3.7 + - - -
511B VAL* 3.4 34.6 - - - +
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Residues in contact with VAL 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 TYR* 3.1 51.5 + - + +
26A ALA 3.8 3.8 - - - +
27A MET 3.3 0.2 - - - -
28A SER* 1.3 77.0 - - - +
30A ILE* 1.3 62.5 + - - +
33A ARG* 3.5 29.5 + - - +
34A ALA* 3.1 34.9 + - + +
175A ILE 4.5 1.8 - - - +
176A ALA* 3.6 32.1 - - + -
177A VAL* 3.9 9.9 - - + +
511B VAL* 6.1 0.2 - - + -
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Residues in contact with ILE 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 ALA 3.0 22.5 + - - +
27A MET* 3.8 6.1 - - - +
29A VAL* 1.3 75.8 - - - +
31A VAL* 1.3 67.1 + - + +
35A LEU* 3.3 38.1 + - + +
176A ALA* 4.3 8.3 - - + -
177A VAL 3.4 26.5 - - - +
179A MET* 3.7 21.3 - - + -
338A LEU* 3.6 3.7 - - + +
343A PRO* 3.7 34.8 - - + -
633B ILE* 3.8 25.6 - - + -
639B TYR* 4.7 3.6 - - + +
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Residues in contact with VAL 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* 3.0 28.4 + - + +
28A SER* 4.3 2.0 - - - +
30A ILE* 1.3 84.8 - - + +
32A ALA* 1.3 68.0 + - + +
33A ARG 3.9 0.7 - - - -
35A LEU 5.5 0.9 - - - -
44A PRO* 4.7 5.0 - - - +
338A LEU* 3.7 24.6 - - + +
341A GLY* 3.8 14.1 - - - +
639B TYR* 3.6 33.7 - - + -
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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 SER* 2.7 27.3 + - - +
31A VAL* 1.3 83.6 - - + +
33A ARG* 1.3 66.9 + - - +
44A PRO* 3.8 21.4 - - + +
48A ARG* 6.0 2.9 - - - +
79A HIS* 6.0 1.4 - - - -
81A HIS* 5.7 3.3 + - - -
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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
------------------------------------------------------------
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