Contacts of the helix formed by residues 87 - 101 (chain C) in PDB entry 5WYF
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 HIS 87 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C LEU* 4.3 12.1 - - + -
80C TYR* 3.4 26.2 - - + -
82C PRO* 3.7 10.8 - - + +
86C HIS* 1.3 76.2 - - - +
88C VAL* 1.3 62.9 + - - +
89C PRO* 3.5 10.3 - - + +
90C GLY* 3.1 31.9 + - - -
91C MET* 3.3 24.4 + - - +
312C GLY 2.7 28.7 + - - -
314C PRO* 3.5 30.3 - - + +
317C SER* 3.8 1.3 - - - -
14D GLU* 5.2 0.4 + - - +
30D VAL* 4.4 3.1 - - - -
31D ILE* 3.8 16.8 - - + +
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Residues in contact with VAL 88 (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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87C HIS* 1.3 71.1 - - - +
89C PRO* 1.3 70.5 - - + +
91C MET* 3.4 8.5 + - + +
92C GLU* 3.0 49.7 + - + +
10D LEU* 4.6 17.5 - - + -
30D VAL* 4.4 7.6 - - + -
31D ILE 4.6 3.8 + - - +
32D ASP* 5.6 4.0 - - - +
42D VAL* 3.7 30.1 - - + -
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Residues in contact with PRO 89 (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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73C GLN* 3.6 30.7 - - - +
87C HIS* 3.5 13.9 - - + +
88C VAL* 1.3 95.7 - - + +
90C GLY* 1.3 54.5 + - - +
92C GLU* 4.6 2.2 - - + +
93C LEU* 3.0 30.0 + - - +
314C PRO* 4.0 7.9 - - + +
317C SER* 3.7 18.6 - - - -
318C ALA* 4.1 10.3 - - + +
321C LEU* 3.6 18.7 - - + +
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Residues in contact with GLY 90 (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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82C PRO* 6.1 0.7 - - - -
87C HIS* 3.1 29.6 + - - -
89C PRO* 1.3 71.9 - - - +
91C MET* 1.3 55.5 + - - +
93C LEU* 3.3 1.3 + - - -
94C SER* 2.7 38.5 + - - -
111C PHE* 3.7 14.6 - - - -
312C GLY 5.3 0.2 - - - -
317C SER* 3.8 9.6 - - - -
14D GLU* 5.3 2.2 - - - -
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Residues in contact with MET 91 (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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86C HIS* 3.6 14.8 - - + -
87C HIS 3.3 25.1 + - - +
88C VAL* 3.6 12.6 - - + +
90C GLY* 1.3 75.0 - - - +
92C GLU* 1.3 62.1 + - + +
94C SER* 3.0 20.7 + - - -
95C GLU* 3.4 13.5 + - - +
10D LEU* 3.6 47.1 - - + +
11D ILE* 3.7 10.5 - - + +
14D GLU* 3.4 46.9 + - + +
17D TYR* 5.9 0.2 - - - -
30D VAL* 3.9 10.5 - - + -
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Residues in contact with GLU 92 (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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88C VAL* 3.0 38.9 + - + +
89C PRO* 3.8 4.7 - - - +
91C MET* 1.3 76.8 - - + +
93C LEU* 1.3 58.8 + - - +
95C GLU* 3.4 7.7 + - - +
96C LYS* 3.0 26.9 + - - +
321C LEU* 3.6 25.8 - - + +
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Residues in contact with LEU 93 (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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89C PRO 3.0 14.0 + - - +
90C GLY 3.7 2.5 - - - +
92C GLU* 1.3 78.0 - - - +
94C SER* 1.3 65.7 + - - +
96C LYS* 3.0 3.2 + - + +
97C LEU* 2.9 41.5 + - + +
111C PHE* 3.5 18.2 - - + -
288C LEU* 3.7 25.4 - - + -
317C SER* 3.9 15.0 - - - +
320C SER* 3.5 26.2 - - - +
321C LEU* 4.1 17.2 - - + +
324C LEU* 3.6 23.8 - - + -
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Residues in contact with SER 94 (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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90C GLY 2.7 19.8 + - - -
91C MET* 3.0 21.0 + - - -
93C LEU* 1.3 73.5 - - - +
95C GLU* 1.3 59.8 + - - +
98C ALA* 3.2 18.2 + - - +
109C VAL* 3.4 21.1 - - - +
111C PHE* 3.9 11.3 - - - -
14D GLU* 4.3 5.2 - - - +
17D TYR* 4.4 9.4 - - - +
18D TYR* 3.9 37.7 - - - +
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Residues in contact with GLU 95 (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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91C MET 3.4 10.4 + - - +
92C GLU* 3.7 9.3 - - - +
93C LEU 3.2 0.4 - - - -
94C SER* 1.3 79.0 + - - +
96C LYS* 1.3 66.9 + - - +
98C ALA* 3.5 2.4 + - - +
99C LYS* 2.5 60.1 + - + +
1010C CD 2.5 26.4 - - - -
13D GLU* 4.5 6.1 - - - +
17D TYR* 3.6 33.0 - - + -
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Residues in contact with LYS 96 (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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92C GLU 3.0 16.2 + - - +
93C LEU* 3.0 7.8 + - + +
95C GLU* 1.3 76.0 - - - +
97C LEU* 1.3 58.1 + - - +
99C LYS* 3.2 6.6 + - - -
100C ILE* 2.8 52.9 + - + +
321C LEU* 4.1 22.9 - - + -
324C LEU* 4.1 30.3 + - + +
325C ASP* 4.0 21.2 + - - -
328C GLU* 4.9 8.9 + - - +
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Residues in contact with LEU 97 (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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93C LEU* 2.9 44.0 + - + +
94C SER 3.8 3.4 - - - +
96C LYS* 1.3 75.8 - - - +
98C ALA* 1.3 64.3 + - - +
100C ILE* 3.8 19.4 - - + +
101C ALA* 3.0 28.1 + - - +
109C VAL* 4.0 11.2 - - + -
111C PHE* 3.8 20.6 - - + -
256C LEU* 5.9 0.2 - - + -
263C TRP* 5.5 4.5 - - + -
278C VAL* 5.0 4.7 - - + -
282C LEU* 4.0 25.8 - - + -
290C ALA* 4.2 15.5 - - + -
292C ILE* 4.1 18.0 - - + +
324C LEU* 4.4 3.8 - - + -
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Residues in contact with ALA 98 (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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94C SER 3.2 11.4 + - - +
95C GLU 3.7 8.5 - - - +
97C LEU* 1.3 79.0 - - - +
99C LYS* 1.3 58.9 + - - +
101C ALA* 3.9 8.1 - - - +
107C LYS* 3.6 52.1 + - - +
108C MET* 4.6 0.2 - - - -
109C VAL* 3.6 11.7 - - + +
292C ILE* 4.6 1.1 - - - -
17D TYR* 3.9 18.8 - - + -
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Residues in contact with LYS 99 (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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95C GLU* 2.5 50.3 + - + +
96C LYS* 3.7 5.6 - - + +
97C LEU 3.2 0.4 - - - -
98C ALA* 1.3 80.9 - - + +
100C ILE* 1.3 64.5 + - + +
101C ALA 3.6 6.8 + - - +
1010C CD 4.2 2.6 - - - -
17D TYR* 3.4 28.9 + - + -
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Residues in contact with ILE 100 (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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96C LYS* 2.8 45.2 + - + +
97C LEU* 3.8 20.4 - - + +
99C LYS* 1.3 72.1 - - + +
101C ALA* 1.3 69.3 + - - +
256C LEU* 5.2 0.4 - - + -
262C MET* 4.9 18.1 - - + +
263C TRP* 3.1 31.2 + - + -
266C GLN* 5.7 0.3 + - - -
324C LEU* 4.0 32.3 - - + -
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Residues in contact with ALA 101 (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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97C LEU 3.0 18.6 + - - +
98C ALA 3.9 3.3 - - - +
99C LYS 3.4 7.1 - - - +
100C ILE* 1.3 81.5 - - - +
102C PRO* 1.4 75.0 - - + +
103C GLY 3.5 8.8 + - - +
107C LYS* 3.8 27.7 + - + -
263C TRP* 4.0 6.7 - - - +
276C MET* 4.4 3.8 - - - -
292C ILE* 3.8 14.4 - - + -
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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