Contacts of the helix formed by residues 88 - 101 (chain D) 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 VAL 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C LEU* 4.5 16.4 - - + -
30C VAL* 4.4 7.6 - - + -
31C ILE 4.4 3.6 + - - +
32C ASP* 5.5 2.9 - - - +
42C VAL* 3.8 29.4 - - + -
87D HIS* 1.3 70.0 - - - +
89D PRO* 1.4 78.2 - - + +
91D MET* 3.2 8.5 + - + +
92D GLU* 2.9 47.1 + - + +
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Residues in contact with PRO 89 (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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31C ILE 5.8 0.2 - - - +
73D GLN* 3.5 31.4 - - - +
87D HIS* 3.6 14.6 - - + +
88D VAL* 1.4 95.4 - - + +
90D GLY* 1.3 55.6 + - - +
92D GLU* 4.7 0.9 - - + +
93D LEU* 3.0 29.6 + - - +
314D PRO* 3.8 9.2 - - + +
317D SER* 3.6 20.0 - - - -
318D ALA* 3.9 9.9 - - + +
321D LEU* 3.7 16.4 - - + +
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Residues in contact with GLY 90 (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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14C GLU* 5.2 2.7 - - - -
82D PRO* 6.1 1.1 - - - -
87D HIS* 3.2 27.8 + - - -
88D VAL 3.2 0.6 - - - -
89D PRO* 1.3 74.5 - - - +
91D MET* 1.3 65.5 + - - +
93D LEU* 3.3 1.2 + - - -
94D SER* 2.9 27.8 + - - -
111D PHE* 3.7 13.1 - - - -
312D GLY 5.0 0.4 - - - -
317D SER* 3.8 9.6 - - - -
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Residues in contact with MET 91 (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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10C LEU* 3.6 49.6 - - + +
11C ILE* 3.6 9.6 - - + +
14C GLU* 3.4 44.5 + - + +
30C VAL* 4.1 13.0 - - + -
86D HIS* 3.6 17.0 - - + -
87D HIS 3.2 26.8 + - - +
88D VAL* 3.5 11.7 - - + +
90D GLY* 1.3 74.2 - - - +
92D GLU* 1.3 65.2 + - + +
94D SER* 3.2 16.4 + - - -
95D GLU* 3.3 14.1 + - - +
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Residues in contact with GLU 92 (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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10C LEU* 6.6 0.2 - - + -
88D VAL* 2.9 37.2 + - + +
89D PRO* 4.0 3.8 - - - +
91D MET* 1.3 78.0 - - + +
93D LEU* 1.3 64.2 + - - +
95D GLU* 3.5 6.9 + - - +
96D LYS* 3.0 22.7 + - - +
321D LEU* 3.9 24.1 - - + +
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Residues in contact with LEU 93 (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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89D PRO 3.0 18.0 + - - +
90D GLY 3.9 3.1 - - - +
92D GLU* 1.3 77.0 - - - +
94D SER* 1.3 52.3 + - - +
96D LYS* 3.1 3.0 + - + +
97D LEU* 2.8 45.9 + - + +
111D PHE* 3.8 16.6 - - + -
288D LEU* 3.5 32.8 - - + -
317D SER* 4.0 11.7 - - - +
320D SER* 3.3 28.9 - - - +
321D LEU* 3.8 20.8 - - + +
324D LEU* 3.7 22.9 - - + -
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Residues in contact with SER 94 (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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14C GLU* 4.4 4.2 + - - +
17C TYR* 4.5 4.9 - - - +
18C TYR* 3.7 42.0 + - - +
90D GLY 2.9 14.8 + - - -
91D MET* 3.2 13.5 + - - -
93D LEU* 1.3 75.8 - - - +
95D GLU* 1.3 63.0 + - - +
97D LEU* 3.3 0.8 + - - -
98D ALA* 2.9 23.9 + - - +
109D VAL* 3.6 15.9 - - - +
111D PHE* 3.7 14.0 - - - -
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Residues in contact with GLU 95 (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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13C GLU* 4.6 7.3 - - - +
17C TYR* 3.7 41.1 - - + +
91D MET 3.3 9.9 + - - +
92D GLU* 3.6 10.4 - - - +
94D SER* 1.3 83.0 + - - +
96D LYS* 1.3 63.2 + - - +
98D ALA* 3.3 3.6 + - - +
99D LYS* 3.2 46.9 + - + +
1009D CD 2.5 30.1 - - - -
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Residues in contact with LYS 96 (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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92D GLU 3.0 17.9 + - - +
93D LEU* 3.6 5.8 - - - +
95D GLU* 1.3 76.6 - - - +
97D LEU* 1.3 59.2 + - - +
99D LYS* 3.1 8.8 + - + +
100D ILE* 2.9 43.4 + - + +
321D LEU* 4.5 14.0 + - + -
324D LEU* 4.0 35.3 + - + +
325D ASP* 3.2 26.8 + - - +
328D GLU* 5.1 6.5 + - - +
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Residues in contact with LEU 97 (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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93D LEU* 2.8 28.5 + - + +
94D SER 3.8 4.3 - - - +
96D LYS* 1.3 73.2 - - - +
98D ALA* 1.3 62.5 + - - +
99D LYS 3.0 1.2 + - - -
100D ILE* 3.3 22.0 + - + +
101D ALA* 3.2 24.3 + - - +
109D VAL* 4.3 6.5 - - + -
111D PHE* 3.8 28.9 - - + -
263D TRP* 5.6 4.0 - - + -
278D VAL* 5.3 3.6 - - + -
282D LEU* 3.6 33.4 - - + -
290D ALA* 3.9 19.3 - - + -
292D ILE* 4.0 19.5 - - + +
324D LEU* 4.2 8.5 - - + -
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Residues in contact with ALA 98 (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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17C TYR* 4.0 18.6 - - + -
94D SER 2.9 17.5 + - - +
95D GLU 3.6 6.1 - - - +
96D LYS 3.3 0.2 - - - -
97D LEU* 1.3 76.3 - - - +
99D LYS* 1.3 59.7 + - + +
101D ALA* 4.1 1.6 - - - +
105D SER 5.5 0.2 - - - +
107D LYS* 3.5 52.9 + - - +
109D VAL* 3.6 16.2 - - + +
292D ILE* 4.6 1.8 - - - -
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Residues in contact with LYS 99 (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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17C TYR* 4.0 25.0 + - + -
95D GLU* 3.2 40.3 + - + +
96D LYS* 3.1 11.5 + - + +
97D LEU 3.0 0.6 - - - -
98D ALA* 1.3 78.8 - - + +
100D ILE* 1.3 65.9 + - + +
101D ALA 3.3 9.5 + - - +
1009D CD 4.5 2.8 - - - -
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Residues in contact with ILE 100 (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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96D LYS* 2.9 36.8 + - + +
97D LEU* 3.8 22.2 - - + +
99D LYS* 1.3 76.6 - - + +
101D ALA* 1.3 66.8 + - - +
102D PRO* 4.6 0.2 - - - +
262D MET* 4.7 18.5 - - + +
263D TRP* 3.0 32.9 + - + -
266D GLN* 5.7 0.5 + - - -
292D ILE* 6.2 0.2 - - + -
324D LEU* 3.9 34.1 - - + -
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Residues in contact with ALA 101 (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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97D LEU 3.2 11.0 + - - +
98D ALA 4.1 1.5 - - - +
99D LYS 3.3 7.0 - - - +
100D ILE* 1.3 80.5 - - - +
102D PRO* 1.3 77.3 - - + +
103D GLY 3.2 10.7 + - - +
107D LYS* 3.5 29.3 + - + -
263D TRP* 3.9 5.8 - - - +
276D MET* 4.3 6.1 - - - -
292D ILE* 3.7 21.1 - - + -
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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