Contacts of the helix formed by residues 65 - 77 (chain D) in PDB entry 5SY1
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 ASP 65 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625B SER 4.3 0.9 - - - +
626B ARG* 3.3 39.5 + - - +
629B PHE* 3.3 29.3 - - - +
630B GLN* 4.1 6.5 - - - +
17D PHE* 4.4 1.8 - - - -
26D GLY 4.0 7.4 - - - +
27D THR* 4.7 1.1 - - - -
59D ASP* 5.5 0.7 - - - +
64D ILE* 1.3 80.2 - - - +
66D PHE* 1.3 79.0 + - - +
67D PRO* 3.5 10.5 - - + +
68D GLU* 2.9 29.1 + - + +
69D PHE* 2.8 23.6 + - - +
204D CA 3.9 3.5 - - - -
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Residues in contact with PHE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622B LEU* 4.0 29.4 - - + -
625B SER* 5.3 4.5 - - - +
629B PHE* 6.2 3.1 - - + -
10D ILE* 4.3 12.3 - - + -
13D PHE* 3.2 37.5 - - + -
14D LYS* 3.6 45.3 - - + +
17D PHE* 3.8 36.8 - + + -
26D GLY 4.3 1.3 + - - +
65D ASP* 1.3 81.3 + - - +
67D PRO* 1.3 69.0 - - + +
69D PHE* 3.0 12.3 + + - +
70D LEU* 2.8 32.9 + - + +
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Residues in contact with PRO 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B LEU* 4.4 9.0 - - + +
615B THR* 5.3 6.3 - - + -
616B LEU* 4.7 13.2 - - + -
622B LEU* 4.6 20.2 - - + +
625B SER* 4.8 2.5 - - - +
626B ARG* 4.0 30.1 - - + +
65D ASP* 3.5 17.9 - - - +
66D PHE* 1.3 96.2 - - + +
68D GLU* 1.3 62.3 + - - +
70D LEU* 3.8 9.5 - - + +
71D THR* 3.3 30.4 + - + +
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Residues in contact with GLU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B LEU* 4.3 18.6 - - + +
626B ARG* 5.3 5.4 + - - +
56D VAL* 3.6 26.7 - - - +
57D ASP* 3.0 12.0 - - - +
58D ALA* 4.2 7.1 - - + +
59D ASP* 2.6 26.0 + - - +
63D THR 3.1 3.5 - - - +
64D ILE* 3.3 7.1 - - + -
65D ASP* 2.9 30.6 + - + +
66D PHE 3.2 0.6 - - - -
67D PRO* 1.3 78.9 - - - +
69D PHE* 1.3 61.8 + - - +
71D THR* 3.3 15.5 + - - -
72D MET* 3.6 5.4 - - - +
116D LYS* 5.2 1.0 + - - -
204D CA 2.4 30.7 - - - -
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Residues in contact with PHE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559B VAL* 4.9 3.6 - - + -
560B MET* 5.7 0.2 - - - -
563B PHE* 3.4 56.8 - + + -
13D PHE* 3.9 36.6 - + + -
16D ALA* 4.9 7.4 - - + -
17D PHE* 3.9 33.0 - + + -
20D PHE* 4.3 15.0 - + - -
28D ILE* 5.2 4.3 - - + -
56D VAL* 4.8 2.5 - - - -
64D ILE* 4.1 7.8 - - + +
65D ASP 2.8 14.0 + - - +
66D PHE* 3.0 14.8 + + - +
68D GLU* 1.3 76.2 - - - +
70D LEU* 1.3 66.2 + - - +
71D THR 3.5 0.3 + - - -
72D MET* 3.7 10.2 + - - +
73D MET* 3.9 16.3 + - + +
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B THR* 3.9 25.6 - - + -
619B ASN* 4.5 7.0 - - - +
622B LEU* 4.2 20.0 - - + -
2D ALA 5.9 1.8 - - - +
5D LEU* 4.7 15.0 - - + -
10D ILE* 5.5 4.7 - - + -
13D PHE* 3.5 39.7 - - + -
66D PHE* 2.8 24.9 + - + +
67D PRO* 3.8 8.7 - - + +
68D GLU 3.3 0.4 - - - -
69D PHE* 1.3 81.7 - - - +
71D THR* 1.3 58.7 + - + +
72D MET 3.3 0.3 + - - -
73D MET* 3.4 4.8 + - + +
74D ALA* 3.0 30.3 + - + +
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Residues in contact with THR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611B GLN* 3.8 21.5 - - + +
612B LEU* 4.7 10.7 - - + +
615B THR* 3.3 30.5 - - + +
2D ALA* 6.0 0.4 - - + -
56D VAL 5.5 0.9 + - - -
67D PRO 3.3 14.0 + - - +
68D GLU* 3.3 14.6 + - - -
70D LEU* 1.3 74.3 - - - +
72D MET* 1.3 66.9 + - - +
74D ALA* 3.6 8.3 - - + +
75D ARG* 3.0 46.5 + - - +
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Residues in contact with MET 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B PHE* 4.4 14.4 - - + -
566B LEU* 4.0 21.4 - - + +
567B LEU* 4.9 9.4 - - + -
55D GLU* 4.2 28.3 - - + +
56D VAL* 3.7 45.5 - - + +
68D GLU 3.6 16.8 - - - +
69D PHE 3.7 7.6 + - - +
70D LEU 3.2 0.6 - - - -
71D THR* 1.3 80.4 + - - +
73D MET* 1.3 63.8 + - - +
75D ARG* 2.8 43.2 + - - +
76D LYS* 4.1 15.5 + - - +
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Residues in contact with MET 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B VAL* 3.7 43.7 - - + +
233B LEU* 4.3 4.4 - - - +
559B VAL* 4.8 5.4 - - + +
562B ALA 4.1 13.9 - - - +
563B PHE* 3.7 32.5 - - + +
566B LEU* 3.7 18.4 - - - -
13D PHE* 4.9 17.2 - - + -
69D PHE* 3.9 21.0 + - + +
70D LEU* 3.4 7.2 + - - +
72D MET* 1.3 77.2 - - - +
74D ALA* 1.3 61.5 + - - +
75D ARG 3.4 0.4 + - - -
76D LYS 4.5 0.4 - - - -
77D MET* 4.0 40.1 + - + +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B LEU* 3.8 13.3 - - + +
615B THR* 5.4 0.2 - - - +
2D ALA* 3.4 37.2 + - + +
70D LEU* 3.0 23.9 + - + +
71D THR* 3.6 11.2 - - + +
72D MET 3.2 0.8 - - - -
73D MET* 1.3 77.0 - - - +
75D ARG* 1.3 65.7 + - - +
77D MET 4.7 0.2 - - - -
78D LYS* 3.6 22.7 - - - +
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Residues in contact with ARG 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B LYS* 5.3 15.2 - - - +
607B ARG* 6.2 0.2 - - - +
608B ALA* 4.2 23.4 + - - +
611B GLN* 2.5 40.2 + - - +
55D GLU 5.0 5.2 + - - -
56D VAL 5.6 2.0 + - - -
71D THR* 3.0 30.6 + - - +
72D MET* 2.8 51.0 - - - +
73D MET 3.4 0.8 - - - -
74D ALA* 1.3 80.0 - - - +
76D LYS* 1.3 83.8 + - + +
77D MET 3.6 1.0 + - - -
78D LYS* 3.8 13.5 + - - +
148D SER 6.0 1.6 - - - -
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Residues in contact with LYS 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LYS* 4.7 3.8 + - - -
566B LEU* 4.1 31.5 + - + +
570B SER* 4.9 13.3 - - - -
55D GLU* 3.8 20.8 + - - -
72D MET* 4.1 15.3 + - - +
73D MET 4.2 0.8 + - - -
75D ARG* 1.3 99.0 - - + +
77D MET* 1.3 74.9 + - - +
78D LYS 3.5 2.1 - - - +
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Residues in contact with MET 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ARG* 4.0 45.3 - - + +
229B VAL* 4.5 10.8 - - + +
230B LYS* 3.7 42.8 + - - +
233B LEU* 4.4 10.7 - - + +
234B LYS* 5.5 2.3 + - - +
562B ALA* 5.1 4.0 - - + +
566B LEU* 3.8 35.9 - - + -
73D MET* 4.0 34.3 + - + +
75D ARG 3.5 0.6 - - - -
76D LYS* 1.3 91.9 - - - +
78D LYS* 1.3 65.4 + - - +
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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