Contacts of the helix formed by residues 14 - 32 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ARG 3.5 2.0 + - - -
13C ASN* 1.3 72.5 - - - +
15C THR* 1.3 69.6 + - - +
17C GLU* 3.8 6.0 - - - +
18C MET* 3.1 26.5 + - + +
521D LEU* 4.6 14.6 - - + +
525D TYR* 4.2 5.2 - - + -
532D ILE* 3.9 31.2 - - + -
606D VAL* 3.7 24.0 - - + -
607D LYS 3.0 19.5 + - - +
608D LEU* 4.0 27.4 - - + -
614D ALA* 4.9 4.3 - - + -
618D PHE* 3.6 31.2 - - + -
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Residues in contact with THR 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ASN* 3.3 15.3 + - - +
14C ILE* 1.3 79.7 - - - +
16C SER* 1.3 63.9 + - - +
18C MET* 3.6 5.0 + - - +
19C ARG* 3.2 36.6 + - - +
608D LEU* 5.6 0.3 - - - +
610D ASP 4.7 2.8 + - - -
613D GLU* 3.9 28.5 + - + +
614D ALA* 3.8 27.7 + - - +
617D THR* 3.3 24.6 - - - +
618D PHE* 5.9 1.1 - - - -
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Residues in contact with SER 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ARG* 4.1 17.3 - - - -
13C ASN* 3.2 25.4 + - - +
15C THR* 1.3 76.7 - - - +
17C GLU* 1.3 58.3 + - - +
19C ARG* 3.3 6.6 + - - +
20C GLU* 2.9 41.1 + - - +
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Residues in contact with GLU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ARG* 2.7 47.5 + - + +
13C ASN 3.0 16.6 + - - +
14C ILE* 3.8 8.3 - - - +
15C THR 3.4 0.2 - - - -
16C SER* 1.3 77.2 - - - +
18C MET* 1.3 55.7 + - - +
21C SER* 2.8 53.6 + - - -
517D ARG* 2.8 23.4 + - - -
521D LEU* 3.7 18.4 - - + -
539D ILE* 3.6 26.6 - - + +
604D LEU* 5.4 2.4 - - - +
606D VAL* 5.9 0.7 - - + -
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Residues in contact with MET 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE 3.1 21.9 + - - +
15C THR 3.8 4.3 - - - +
17C GLU* 1.3 77.3 - - - +
19C ARG* 1.3 56.6 + - - +
22C PHE* 3.1 35.5 + - - +
518D THR* 3.8 38.2 - - - +
521D LEU* 3.9 15.0 - - + -
522D THR* 3.6 13.9 - - - +
617D THR* 4.1 7.0 - - + -
618D PHE* 3.6 47.1 - - + -
621D LEU* 3.4 19.6 - - + +
622D MET* 3.8 16.2 - - + -
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Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C THR* 3.2 33.8 + - - +
16C SER* 3.9 6.7 - - - +
18C MET* 1.3 76.9 - - - +
20C GLU* 1.3 61.2 + - + +
23C LEU* 3.1 30.4 + - - +
617D THR* 4.0 15.4 + - + -
620D MET* 3.9 12.7 - - + +
621D LEU* 4.1 6.3 - - + -
632D PHE* 3.3 41.8 - - + -
636D ASN* 3.6 25.1 + - - +
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Residues in contact with GLU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ARG* 2.8 40.5 + - - +
16C SER* 2.9 22.8 + - - +
19C ARG* 1.3 78.1 - - + +
21C SER* 1.3 61.6 + - - +
23C LEU* 3.5 6.2 + - + +
24C ASP* 3.0 29.1 + - - +
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ARG* 5.4 0.2 + - - -
17C GLU* 2.8 41.0 + - - -
20C GLU* 1.3 74.1 - - - +
22C PHE* 1.3 61.5 + - - +
24C ASP* 3.3 7.9 + - - +
25C TYR* 3.0 27.5 + - - +
514D ALA* 3.8 21.1 - - - +
517D ARG* 3.8 11.5 + - - -
518D THR* 3.7 17.9 - - - -
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Residues in contact with PHE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C MET 3.1 21.3 + - - +
19C ARG 4.7 0.2 - - - +
21C SER* 1.3 74.1 - - - +
23C LEU* 1.3 56.5 + - - +
25C TYR* 3.3 7.0 + + - +
26C ALA* 2.7 41.7 + - + +
177C VAL* 3.7 22.7 - - + -
515D HIS* 4.2 20.9 - + - +
518D THR* 3.9 16.3 - - + +
621D LEU* 3.3 46.0 - - + -
622D MET* 3.7 24.5 - - + -
629D ARG* 3.6 28.5 - - + -
632D PHE* 5.0 3.6 - + - -
633D ILE* 5.5 0.7 - - + -
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG 3.1 21.7 + - - +
20C GLU* 3.8 5.8 - - + +
21C SER 3.3 0.2 - - - -
22C PHE* 1.3 74.7 - - - +
24C ASP* 1.3 60.7 - - - +
26C ALA* 4.3 3.4 - - + -
27C MET* 2.9 59.9 + - + +
632D PHE* 3.9 22.2 - - + -
633D ILE* 4.4 15.5 - - + -
636D ASN* 3.7 39.9 - - + +
637D ALA* 5.3 0.2 - - - -
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Residues in contact with ASP 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLU 3.0 18.6 + - - +
21C SER* 3.3 10.0 + - - +
23C LEU* 1.3 77.7 - - - +
25C TYR* 1.3 60.8 + - - +
27C MET* 4.1 3.8 - - - +
28C SER* 3.3 20.8 + - - -
510D ASP 5.6 0.9 - - - -
511D VAL* 3.9 19.8 + - - +
514D ALA* 4.5 11.5 - - + +
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Residues in contact with TYR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C SER 3.0 15.2 + - - +
22C PHE* 3.8 10.8 - + - +
24C ASP* 1.3 75.6 - - - +
26C ALA* 1.3 66.5 + - - +
28C SER* 3.3 2.4 + - - -
29C VAL* 3.2 45.3 + - + +
33C ARG* 3.9 6.0 + - - -
177C VAL* 3.9 23.1 - - + +
460D LYS* 3.3 18.5 + - - -
511D VAL* 3.3 38.6 + - + +
512D ASP* 3.3 21.8 - - - -
515D HIS* 3.5 42.6 + + + -
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 2.7 26.3 + - + +
23C LEU* 3.2 6.3 + - - +
25C TYR* 1.3 72.5 - - - +
27C MET* 1.3 64.1 + - + +
29C VAL* 3.4 2.4 + - - +
30C ILE* 3.2 29.8 + - + +
177C VAL* 4.0 24.0 - - + +
633D ILE* 3.8 32.1 - - + -
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Residues in contact with MET 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 2.9 35.5 + - + +
24C ASP* 4.1 4.3 - - - +
26C ALA* 1.3 74.6 - - - +
28C SER* 1.3 58.5 + - - +
30C ILE* 3.3 7.1 + - + +
31C VAL* 2.9 39.6 + - + +
633D ILE* 3.9 19.3 - - - -
637D ALA* 3.6 29.6 - - + -
638D VAL 4.2 11.4 - - - +
639D TYR* 3.3 44.2 - - + +
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Residues in contact with SER 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASP* 3.3 16.8 + - - -
25C TYR 3.3 5.5 + - - -
27C MET* 1.3 78.2 - - - +
29C VAL* 1.3 59.8 + - - +
31C VAL* 4.4 5.8 - - - -
32C ALA* 2.8 39.0 + - - +
33C ARG* 4.1 2.4 + - - +
511D VAL* 3.5 35.4 - - - +
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 3.2 50.7 + - + +
26C ALA 4.0 3.4 - - - +
27C MET 3.3 0.2 - - - -
28C SER* 1.3 79.4 - - - +
30C ILE* 1.3 60.1 + - - +
33C ARG* 3.5 32.3 + - - +
34C ALA* 2.9 38.8 + - + +
175C ILE 4.4 2.2 - - - +
176C ALA* 3.8 29.8 - - + -
177C VAL* 4.3 6.1 - - + -
511D VAL* 5.7 0.2 - - + -
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Residues in contact with ILE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ALA 3.2 21.9 + - - +
27C MET* 3.3 8.0 + - - +
29C VAL* 1.3 77.7 - - - +
31C VAL* 1.3 66.7 + - + +
35C LEU* 3.3 38.3 + - + +
176C ALA* 4.3 9.4 - - + -
177C VAL 3.7 23.3 - - - +
179C MET* 3.9 21.1 - - + -
338C LEU* 3.5 3.6 - - - +
343C PRO* 3.7 33.7 - - + -
633D ILE* 4.0 22.9 - - + -
639D TYR* 4.8 2.9 - - + +
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C MET* 2.9 26.1 + - + +
28C SER* 4.4 4.5 - - - +
30C ILE* 1.3 85.1 - - + +
32C ALA* 1.3 65.2 + - + +
33C ARG 3.9 0.9 - - - -
35C LEU 5.3 0.4 - - - +
44C PRO* 4.8 1.0 - - - +
338C LEU* 3.7 22.4 - - + +
341C GLY* 3.9 13.5 - - - +
501C GOL 4.4 12.1 + - - -
639D TYR* 3.5 35.9 - - + -
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Residues in contact with ALA 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER* 2.8 22.0 + - - +
31C VAL* 1.3 85.3 - - + +
33C ARG* 1.3 63.8 + - - +
44C PRO* 3.3 26.7 - - + +
48C ARG* 5.9 2.6 + - - +
79C HIS* 5.8 1.7 - - - -
81C HIS* 5.8 1.6 + - - -
501C GOL 5.1 9.2 - - - +
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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
------------------------------------------------------------
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