Contacts of the helix formed by residues 88 - 103 (chain A) in PDB entry 1YNU
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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LEU* 4.6 15.9 - - + -
82A PHE* 3.3 33.6 - - + -
87A GLY* 1.3 70.0 - - - -
89A PRO* 1.3 76.0 - - + +
90A ALA* 4.3 11.0 - - + +
91A PHE* 3.1 19.9 + - + +
92A LYS* 3.1 12.3 + - - +
307A SER* 4.8 0.9 - - - +
310A GLN* 2.9 27.9 + - + +
311A HIS* 3.9 42.0 - - + +
314A SER* 4.8 2.2 - - - -
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Residues in contact with PRO 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 4.2 9.0 - - + -
87A GLY 3.1 9.6 - - - +
88A LEU* 1.3 89.9 - - + +
90A ALA* 1.3 63.2 + - + +
92A LYS* 3.3 9.8 + - + +
93A LYS* 3.1 23.9 + - - +
111A PRO* 5.6 0.9 - - - +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS* 4.5 19.5 - - - +
88A LEU* 3.3 9.5 - - + +
89A PRO* 1.3 82.1 - - + +
91A PHE* 1.3 62.0 + - - +
93A LYS* 3.6 5.6 + - - +
94A ALA* 3.1 20.4 + - - +
311A HIS* 6.4 1.1 - - + -
314A SER* 3.3 19.3 + - - +
318A SER* 5.1 0.5 + - - -
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.1 20.1 + - + +
90A ALA* 1.3 78.9 - - - +
92A LYS* 1.3 59.2 + - - +
94A ALA* 3.3 2.4 + - + -
95A MET* 2.9 51.3 + - + +
116A LEU* 3.6 31.0 - - + -
271A LEU* 4.3 0.9 - - + -
282A VAL* 3.7 30.3 - - + -
305A VAL* 5.0 1.3 - - + -
310A GLN* 3.4 43.1 - - + +
313A LEU* 3.5 31.2 - - + -
314A SER* 3.4 14.9 + - - -
317A LEU* 4.2 5.8 - - + -
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS* 2.8 36.0 + - - +
87A GLY 4.5 3.1 - - - -
88A LEU 3.1 13.1 + - - +
89A PRO* 3.3 10.7 + - + +
91A PHE* 1.3 76.1 - - - +
93A LYS* 1.3 58.5 + - - +
95A MET* 3.3 2.3 + - - +
96A VAL* 3.0 34.4 + - - +
111A PRO* 3.0 37.4 + - + +
112A ASN* 4.4 9.1 + - - +
114A LEU* 3.2 39.5 + - + +
115A VAL* 5.4 0.2 - - - +
116A LEU* 4.0 24.5 - - + +
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO 3.1 15.5 + - - +
90A ALA* 3.9 5.8 - - - +
91A PHE 3.2 0.2 - - - -
92A LYS* 1.3 75.4 - - - +
94A ALA* 1.3 65.0 + - - +
96A VAL* 3.0 29.4 - - + +
97A ASP* 3.1 43.5 + - - +
109A PHE 5.5 1.6 + - - -
111A PRO* 4.5 16.9 - - + +
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Residues in contact with ALA 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ALA 3.1 15.1 + - - +
91A PHE* 3.6 6.1 - - + +
93A LYS* 1.3 80.3 - - - +
95A MET* 1.3 56.7 + - - +
97A ASP* 4.0 5.4 - - - +
98A PHE* 3.1 27.5 + - - +
314A SER* 4.0 9.9 - - - +
317A LEU* 3.9 31.7 - - + +
318A SER* 3.9 18.6 - - - +
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Residues in contact with MET 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 2.9 38.6 + - + +
92A LYS 3.5 5.4 - - - +
93A LYS 3.1 0.2 - - - -
94A ALA* 1.3 76.0 - - - +
96A VAL* 1.3 58.6 + - - +
98A PHE* 3.2 3.7 + - - +
99A MET* 3.0 38.5 + - - +
114A LEU* 3.9 14.1 - - + -
116A LEU* 4.5 4.9 - - + -
269A TYR* 4.1 24.9 - - + -
270A SER 5.5 0.9 - - - -
271A LEU* 3.7 30.5 - - + -
282A VAL* 4.2 19.1 - - + +
283A GLY 5.1 1.1 - - - -
284A ALA* 4.2 21.3 - - + -
317A LEU* 4.0 11.2 - - - -
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LYS 3.0 17.2 + - - +
93A LYS* 3.0 37.7 - - + +
95A MET* 1.3 75.5 - - - +
97A ASP* 1.3 63.1 + - - +
99A MET* 3.9 7.4 - - - -
100A ALA* 3.2 24.3 + - - +
109A PHE* 3.6 42.9 + - + +
110A ASP 4.3 0.9 - - - -
111A PRO* 3.9 26.0 - - + -
114A LEU* 4.0 18.4 - - + -
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LYS* 3.1 52.6 + - - +
94A ALA* 4.0 5.9 - - - +
95A MET 3.1 0.2 - - - -
96A VAL* 1.3 77.9 - - - +
98A PHE* 1.3 61.8 + - - +
99A MET 3.2 0.2 - - - -
100A ALA* 3.1 8.0 + - - +
101A GLU* 2.8 30.7 + - - +
105A ASN* 4.7 0.9 - - - +
317A LEU 5.9 0.2 - - - +
320A LYS* 3.9 25.8 + - - +
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA 3.1 19.1 + - - +
95A MET* 3.6 5.2 - - - +
97A ASP* 1.3 77.8 - - - +
99A MET* 1.3 56.0 + - - +
101A GLU* 3.3 8.4 + - - +
102A ILE* 3.0 43.4 + - + +
269A TYR* 3.5 27.6 - + - -
271A LEU* 4.0 22.7 - - + -
274A ASP* 4.2 8.1 - - + -
275A LEU* 3.9 24.0 - - + -
317A LEU* 4.1 23.3 - - + +
320A LYS* 5.3 1.5 - - - +
323A THR* 4.2 23.6 - - + -
326A TYR* 5.6 2.0 - + + -
327A ILE* 3.9 30.3 - - + -
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Residues in contact with MET 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A MET* 3.0 29.6 + - - +
96A VAL* 4.0 5.6 - - - +
98A PHE* 1.3 76.3 - - + +
100A ALA* 1.3 61.4 + - - +
102A ILE* 3.6 5.5 + - - -
103A ARG* 2.9 43.1 + - - +
109A PHE* 3.8 42.0 - - + -
114A LEU* 4.4 22.7 - - + -
267A VAL* 4.7 11.2 - - + -
269A TYR* 3.6 48.9 - - + -
286A TYR* 4.9 3.8 - - + -
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Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A VAL 3.2 18.3 + - - +
97A ASP* 3.1 11.4 + - - +
99A MET* 1.3 78.3 - - - +
101A GLU* 1.3 56.8 + - - +
103A ARG* 3.1 8.6 + - - +
105A ASN* 2.6 43.3 + - - +
107A VAL 3.5 23.1 - - - +
108A THR* 4.9 4.3 - - - -
109A PHE* 4.2 5.1 - - + +
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Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP 2.8 16.1 + - - +
98A PHE* 3.3 9.9 + - + +
100A ALA* 1.3 73.9 - - - +
102A ILE* 1.3 63.8 + - - +
104A GLY* 3.2 12.6 + - - -
105A ASN* 3.6 18.7 + - - +
320A LYS* 4.3 19.4 + - - +
323A THR* 2.8 31.9 + - - -
324A LYS* 4.1 19.4 - - - +
327A ILE* 3.5 26.3 - - + +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 3.0 36.3 + - + +
99A MET* 3.8 7.2 - - - +
100A ALA 3.3 0.2 - - - -
101A GLU* 1.3 77.0 - - - +
103A ARG* 1.3 63.6 + - + +
104A GLY 3.2 3.4 + - - -
234A SER* 3.5 41.0 - - - +
235A GLY* 3.9 10.1 - - - +
243A PHE* 4.6 7.0 - - + +
269A TYR* 3.1 33.0 - - + +
274A ASP* 4.0 7.0 - - + +
327A ILE* 4.3 22.2 - - + -
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A MET* 2.9 42.2 + - - +
100A ALA 3.1 5.0 + - - +
101A GLU 3.1 1.0 - - - -
102A ILE* 1.3 81.3 - - - +
104A GLY* 1.3 62.9 + - - +
105A ASN 3.0 1.3 - - - -
106A LYS* 2.9 34.0 + - + +
107A VAL* 3.4 33.0 - - + -
109A PHE* 3.8 12.5 - - - -
231A GLU* 2.5 45.0 + - - +
234A SER* 3.9 16.9 + - - -
243A PHE* 3.7 22.9 - - + -
245A SER* 3.3 18.0 + - - +
248A GLU* 5.7 1.3 - - - +
267A VAL* 4.5 8.9 - - - +
269A TYR* 4.9 4.2 - - - -
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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
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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