Contacts of the helix formed by residues 88 - 104 (chain A) in PDB entry 2YNU
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 SER 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A LYS* 4.5 10.1 - - - -
86A PRO* 4.0 0.9 - - - +
87A TRP* 1.3 83.0 - - - +
89A GLU* 1.3 63.7 + - - +
90A GLU* 3.7 22.7 + - - +
91A ASP* 3.1 30.9 + - - +
92A THR* 3.0 28.8 + - - -
123A ALA* 3.8 9.0 - - - -
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Residues in contact with GLU 89 (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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88A SER* 1.3 75.2 - - - +
90A GLU* 1.3 73.1 + - + +
92A THR* 3.4 7.1 + - - -
93A LYS* 3.2 32.3 + - - +
123A ALA* 4.5 12.7 - - - +
124A GLY* 5.2 0.4 - - - -
126A LYS* 2.9 38.2 + - - +
127A LEU* 4.0 30.8 - - + +
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Residues in contact with GLU 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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88A SER* 3.7 16.8 + - - +
89A GLU* 1.3 96.5 + - + +
91A ASP* 1.3 64.8 + - - +
93A LYS* 3.5 11.9 + - - +
94A LEU* 3.3 26.9 + - + +
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Residues in contact with ASP 91 (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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40A LYS 4.4 8.3 - - - +
41A PRO* 4.0 3.6 - - - +
42A LEU* 3.2 38.0 + - + +
57A SER* 3.7 15.9 - - - -
58A PHE 4.5 7.1 + - - +
86A PRO* 3.7 20.2 - - + -
87A TRP* 5.8 0.3 - - - +
88A SER* 3.1 21.1 + - - +
90A GLU* 1.3 76.1 - - - +
92A THR* 1.3 63.8 + - - +
94A LEU* 3.4 17.8 + - - +
95A LEU* 3.0 22.0 + - - +
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Residues in contact with THR 92 (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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82A ILE* 6.0 1.3 - - + -
85A THR* 4.9 0.7 - - - -
86A PRO* 3.2 26.6 - - + +
88A SER 3.0 18.3 + - - -
89A GLU 3.6 5.6 - - - -
90A GLU 3.3 0.2 - - - -
91A ASP* 1.3 76.3 - - - +
93A LYS* 1.3 59.7 + - - +
95A LEU* 3.1 4.6 + - + +
96A LEU* 2.8 27.8 + - + +
124A GLY* 3.2 34.9 + - - +
127A LEU* 3.9 16.6 - - + -
128A LEU* 4.1 20.0 - - + -
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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
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89A GLU* 3.2 24.1 + - - +
90A GLU* 3.8 10.8 - - - +
91A ASP 3.3 0.4 - - - -
92A THR* 1.3 80.6 - - - +
94A LEU* 1.3 57.1 + - + +
96A LEU* 3.3 7.8 + - + +
97A SER* 2.9 37.0 + - - +
127A LEU* 3.9 24.7 - - + +
131A LYS* 5.0 13.0 - - - +
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Residues in contact with LEU 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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41A PRO* 4.3 12.8 - - + -
42A LEU* 4.2 21.6 - - + +
90A GLU* 3.3 10.9 + - + +
91A ASP* 3.4 31.4 - - - +
93A LYS* 1.3 80.5 - - + +
95A LEU* 1.3 56.1 + - - +
97A SER* 3.4 8.2 + - - +
98A TRP* 2.9 28.2 + - - +
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Residues in contact with LEU 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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42A LEU* 3.6 19.5 - - + +
44A VAL* 4.2 8.5 - - + -
55A HIS* 3.8 26.9 - - + -
73A VAL* 3.7 23.6 - - + -
82A ILE* 3.8 36.3 - - + +
86A PRO* 3.8 22.2 - - + -
91A ASP 3.0 13.7 + - - +
92A THR* 3.1 9.6 + - + +
94A LEU* 1.3 74.5 - - - +
96A LEU* 1.3 65.2 + - - +
98A TRP* 3.4 10.5 - - + +
99A ALA* 3.1 21.4 + - + +
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Residues in contact with LEU 96 (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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82A ILE* 4.4 7.4 - - + -
92A THR* 2.8 18.4 + - + +
93A LYS* 3.5 9.6 - - + +
95A LEU* 1.3 74.9 - - - +
97A SER* 1.3 56.9 + - - +
99A ALA* 3.2 5.2 + - - +
100A THR* 3.0 36.6 + - + +
109A VAL* 3.7 19.5 - - + -
127A LEU* 3.9 23.6 - - + -
128A LEU* 3.6 27.4 - - + -
131A LYS* 4.2 22.9 - - + +
134A ILE* 3.6 25.1 - - + -
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Residues in contact with SER 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* 2.9 24.6 + - - +
94A LEU* 3.9 9.0 - - - -
96A LEU* 1.3 69.2 - - - +
98A TRP* 1.3 68.3 + - - +
100A THR* 3.6 8.6 + - - -
102A ASP* 2.8 41.8 + - - +
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Residues in contact with TRP 98 (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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42A LEU* 5.6 0.2 - - + -
44A VAL* 3.5 40.9 + - + +
53A TYR* 3.5 53.6 - + - -
73A VAL* 4.2 22.4 - - + -
75A LEU* 4.9 0.4 - - + -
94A LEU 2.9 15.0 + - - +
95A LEU* 3.4 18.2 - - + +
97A SER* 1.3 77.4 - - - +
99A ALA* 1.3 88.0 + - + +
102A ASP* 3.8 1.1 + - - -
104A ARG* 3.0 78.9 + - - +
106A TYR* 4.2 13.7 - + - -
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Residues in contact with ALA 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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73A VAL* 5.6 2.0 - - + -
80A ALA* 4.8 5.6 - - + -
95A LEU* 3.1 9.7 + - + +
96A LEU 3.6 7.2 - - - +
97A SER 3.2 0.4 - - - -
98A TRP* 1.3 96.4 - - + +
100A THR* 1.3 62.2 + - - +
104A ARG* 3.1 7.6 + - - -
106A TYR* 3.0 38.9 + - + +
109A VAL* 4.0 24.0 - - + -
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Residues in contact with THR 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 LEU* 3.0 22.5 + - + +
97A SER* 3.2 9.2 + - - -
99A ALA* 1.3 77.2 - - + +
102A ASP* 1.3 70.3 + - - +
105A GLY* 3.0 14.3 + - - +
106A TYR 3.8 17.0 - - - +
109A VAL* 5.0 8.3 - - + +
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Residues in contact with ASP 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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97A SER* 2.8 30.6 + - - +
98A TRP* 4.1 4.0 - - - +
100A THR* 1.3 82.9 + - - +
104A ARG* 1.3 65.6 + - - +
105A GLY 3.3 0.6 + - - -
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A TYR* 5.8 1.9 + - - -
78A ASN* 4.7 0.9 - - - +
98A TRP* 3.0 81.1 + - - +
99A ALA 3.1 8.3 + - - +
100A THR 3.1 1.0 - - - -
102A ASP* 1.3 84.8 - - - +
105A GLY* 1.3 60.9 + - - +
106A TYR* 3.4 31.1 - - + +
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ASN* 3.6 19.3 + - - +
100A THR 3.0 13.2 + - - -
102A ASP 3.3 1.6 + - - -
104A ARG* 1.3 79.5 - - - +
106A TYR* 1.3 61.4 + - - +
107A GLN* 4.0 0.5 + - - +
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Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A TYR* 5.2 2.8 + - - -
75A LEU* 3.3 44.5 - - + +
77A ASN 4.1 5.2 + - - -
78A ASN* 2.9 41.7 - - - +
80A ALA* 4.1 13.9 - - + -
98A TRP* 4.2 13.5 - + - -
99A ALA* 3.0 21.4 + - + +
100A THR* 3.8 17.3 + - - +
104A ARG* 3.6 38.6 - - + +
105A GLY* 1.3 78.9 - - - +
107A GLN* 1.3 61.0 + - - +
109A VAL 3.7 2.5 + - - -
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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
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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