Contacts of the helix formed by residues 23 - 39 (chain Y) in PDB entry 5MG3
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 LEU 23 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Y ARG* 1.3 79.0 - - + +
24Y LEU* 1.3 62.0 + - - +
25Y PHE 3.3 3.8 + - - -
26Y VAL* 4.0 19.3 - - + -
27Y ILE* 3.3 45.8 + - + +
181Y ARG* 5.9 0.2 - - - +
420Y VAL* 4.0 33.2 - - + +
423Y LEU* 4.2 15.5 - - + -
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Residues in contact with LEU 24 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518G ARG* 5.4 2.9 - - - +
522G LEU* 6.3 3.4 - - + -
20Y LYS 5.3 0.9 - - - +
21Y ARG* 3.5 49.4 - - + +
22Y ARG 3.4 1.8 - - - -
23Y LEU* 1.3 75.2 - - - +
25Y PHE* 1.3 71.5 + - + +
27Y ILE* 5.4 0.9 - - - -
28Y GLY* 3.1 26.4 + - - +
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Residues in contact with PHE 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518G ARG* 3.6 39.3 - - + -
10Y GLN* 4.6 1.6 - - - -
21Y ARG* 3.7 34.1 + - + -
22Y ARG 5.8 0.2 - - - +
24Y LEU* 1.3 94.5 - - + +
26Y VAL* 1.3 66.7 + - + +
27Y ILE 3.5 0.7 - - - -
28Y GLY* 4.1 0.7 - - - -
29Y ALA* 3.9 11.3 + - - +
177Y GLN* 3.3 44.7 + - - +
178Y ILE* 3.9 15.5 - - + +
180Y GLU* 3.9 24.9 - - + -
181Y ARG* 4.0 20.2 - - + -
182Y GLY* 4.2 7.9 - - - +
189Y ILE* 5.5 0.2 - - - +
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Residues in contact with VAL 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Y ARG 4.7 0.9 - - - +
23Y LEU* 3.5 32.2 + - + -
25Y PHE* 1.3 80.6 - - + +
27Y ILE* 1.4 58.3 - - + +
29Y ALA* 4.5 2.2 - - - +
30Y LEU* 3.9 7.8 - - - +
178Y ILE* 4.4 4.7 - - - -
182Y GLY* 3.3 33.0 - - - -
183Y ILE* 3.6 31.9 - - + +
189Y ILE* 4.4 7.4 - - + +
192Y PHE* 3.8 19.0 - - + -
416Y PHE* 4.2 19.5 - - + -
420Y VAL* 4.9 5.6 - - + -
423Y LEU* 4.4 2.7 - - + -
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Residues in contact with ILE 27 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485E MET* 4.8 13.5 - - + -
488E ILE* 4.2 25.4 - - + -
489E LEU* 4.3 14.4 - - + -
492E LEU* 4.6 17.9 - - + -
23Y LEU* 3.3 39.2 + - + +
24Y LEU* 5.4 0.4 - - - -
26Y VAL* 1.4 76.7 - - + +
28Y GLY* 1.3 65.5 + - - +
29Y ALA 3.2 2.0 - - - -
30Y LEU* 3.4 30.5 + - + +
31Y ILE* 3.5 12.4 + - + +
192Y PHE* 5.0 5.8 - - + -
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Residues in contact with GLY 28 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522G LEU* 6.4 1.6 - - - -
24Y LEU* 3.1 25.6 + - - -
25Y PHE* 4.0 0.4 + - - -
26Y VAL 3.7 0.2 - - - -
27Y ILE* 1.3 76.3 - - - +
29Y ALA* 1.4 55.0 + - - +
31Y ILE* 3.4 8.7 + - - +
32Y VAL* 2.7 42.6 + - - +
174Y LEU* 5.7 0.2 - - - -
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Residues in contact with ALA 29 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Y PHE* 3.9 16.2 + - - +
26Y VAL 4.5 2.0 - - - +
28Y GLY* 1.4 76.5 - - - +
30Y LEU* 1.3 67.2 + - + +
32Y VAL* 3.2 2.9 + - - +
33Y PHE* 3.0 29.6 + - - +
174Y LEU* 3.9 41.4 - - + +
177Y GLN* 4.6 4.0 - - - +
189Y ILE* 5.6 7.2 - - + -
193Y ALA* 4.3 11.7 - - + +
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Residues in contact with LEU 30 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485E MET* 4.6 3.4 - - + -
489E LEU* 4.1 20.9 - - + -
26Y VAL 3.9 12.1 - - - +
27Y ILE* 3.5 12.8 - - + +
28Y GLY 3.2 0.4 - - - -
29Y ALA* 1.3 81.0 - - + +
31Y ILE* 1.4 57.8 + - - +
33Y PHE 3.5 1.2 + - - -
34Y ARG* 3.1 32.2 + - - +
189Y ILE* 5.2 0.9 - - + +
192Y PHE* 3.4 73.8 - - + +
193Y ALA* 3.6 15.9 - - + +
196Y VAL* 3.7 25.0 - - + +
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Residues in contact with ILE 31 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489E LEU* 3.9 32.3 - - + +
492E LEU* 3.8 39.7 - - + +
493E ASP* 4.6 6.7 - - + -
496E LEU* 3.7 30.1 - - + -
27Y ILE* 3.5 12.1 + - + +
28Y GLY* 3.4 10.5 + - - +
30Y LEU* 1.4 70.3 - - - +
32Y VAL* 1.4 66.5 + - + +
34Y ARG* 3.2 15.2 + - - +
35Y ILE* 3.1 29.3 + - + +
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Residues in contact with VAL 32 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522G LEU* 4.4 27.6 - - + -
525G THR* 4.1 26.2 - - + -
526G LEU* 3.9 17.6 - - + +
28Y GLY* 2.7 26.4 + - - +
29Y ALA 3.2 4.5 + - - +
31Y ILE* 1.4 73.8 - - + +
33Y PHE* 1.4 61.0 + - - +
35Y ILE* 3.6 15.6 + - + +
36Y GLY 3.8 1.9 + - - -
78Y PHE* 3.6 15.0 - - + -
174Y LEU* 3.7 28.9 - - + -
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Residues in contact with PHE 33 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Y ALA 3.0 14.4 + - - +
30Y LEU 3.8 2.9 - - - +
32Y VAL* 1.4 70.9 - - - +
34Y ARG* 1.4 57.7 + - - +
36Y GLY* 3.1 3.6 + - - -
37Y SER* 2.6 57.8 + - - -
68Y SER 4.3 15.5 - - - -
69Y GLY* 5.0 0.2 - - - -
78Y PHE* 3.8 37.5 - + + -
81Y GLY* 4.7 7.6 - - - -
171Y LEU* 4.4 24.2 - - + -
174Y LEU* 4.9 1.3 - - + +
193Y ALA* 3.1 26.0 - - + +
194Y GLY* 3.2 30.5 - - - -
196Y VAL* 4.0 8.3 - - + -
197Y ALA* 4.0 14.6 - - + -
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Residues in contact with ARG 34 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489E LEU* 4.2 19.2 - - - +
490E TRP* 5.0 0.2 - - - +
493E ASP* 2.6 43.4 + - + +
497E VAL* 4.8 0.4 - - - -
30Y LEU 3.1 22.1 + - - +
31Y ILE* 3.2 24.6 + - - +
33Y PHE* 1.4 77.1 - - - +
35Y ILE* 1.4 62.3 + - - +
37Y SER* 3.4 5.8 - - - +
38Y PHE* 3.1 45.6 + - + -
196Y VAL* 2.8 47.2 + - + +
198Y GLY 3.0 22.2 + - - -
200Y PRO* 3.9 8.1 - - - +
205Y HIS* 3.0 32.1 + - - -
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Residues in contact with ILE 35 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493E ASP* 5.8 0.7 - - + -
496E LEU* 4.3 27.8 - - + -
497E VAL* 3.9 32.8 - - + +
500E VAL* 6.3 1.8 - - + -
526G LEU* 3.4 49.4 - - + -
529G ILE* 3.7 22.2 - - + -
31Y ILE* 3.1 21.9 + - + +
32Y VAL* 3.9 2.0 - - + +
33Y PHE 3.3 0.2 - - - -
34Y ARG* 1.4 78.7 - - + +
36Y GLY* 1.4 56.1 + - - +
37Y SER 3.4 0.2 - - - -
39Y ILE* 3.4 30.0 + - - +
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Residues in contact with GLY 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529G ILE* 5.0 1.3 - - - -
32Y VAL 3.8 3.2 + - - -
33Y PHE 3.1 4.3 + - - -
35Y ILE* 1.4 75.4 - - - +
37Y SER* 1.3 58.1 + - - +
38Y PHE 3.5 0.4 - - - -
39Y ILE* 4.6 3.6 - - - -
76Y SER* 3.4 1.4 - - - -
77Y ILE* 3.3 29.7 + - - -
78Y PHE* 3.0 47.0 + - - -
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Residues in contact with SER 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y PHE* 2.6 59.0 + - - -
34Y ARG* 3.4 8.1 + - - -
36Y GLY* 1.3 76.3 - - - +
38Y PHE* 1.3 56.7 + - - +
68Y SER 5.5 0.7 - - - -
69Y GLY 4.5 3.9 - - - +
74Y ARG* 2.8 30.3 + - - -
76Y SER* 3.1 18.7 + - - -
78Y PHE* 4.8 3.8 - - - +
79Y ALA* 6.3 0.2 - - - -
197Y ALA* 4.1 9.4 - - - +
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Residues in contact with PHE 38 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493E ASP* 3.3 26.9 - - - -
497E VAL* 3.5 31.4 - - + -
498E ARG* 3.9 5.2 - - - -
501E SER* 4.9 6.6 + - - +
34Y ARG* 3.1 34.8 + - + +
36Y GLY 3.5 0.2 - - - -
37Y SER* 1.3 93.4 - - - +
39Y ILE* 1.3 63.0 + - - +
40Y PRO* 3.5 8.8 - - - +
74Y ARG* 3.8 6.2 - - - +
76Y SER* 3.5 2.7 - - - -
197Y ALA* 3.7 11.4 - - - -
205Y HIS* 3.3 48.2 - + + -
206Y THR* 3.2 30.0 - - + +
208Y GLU* 4.3 11.0 - - + -
209Y GLN* 5.0 0.5 - - - +
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Residues in contact with ILE 39 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497E VAL* 3.9 12.6 - - + -
500E VAL* 4.5 3.1 - - + -
501E SER* 3.6 31.0 - - - +
504E THR* 4.5 7.9 - - - +
529G ILE* 3.7 44.4 - - + -
533G VAL* 4.2 13.9 - - + -
536G ASN* 5.1 1.3 - - - +
35Y ILE* 3.4 18.1 + - + +
36Y GLY* 4.4 3.4 - - - +
37Y SER 4.6 0.2 - - - +
38Y PHE* 1.3 75.7 - - - +
40Y PRO* 1.3 89.1 - - + +
74Y ARG* 4.7 0.2 - - - -
76Y SER* 2.8 26.9 + - - -
77Y ILE* 3.8 6.5 + - + -
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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