Contacts of the helix formed by residues 83 - 101 (chain D) in PDB entry 2Y1M
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 TYR 83 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C GLU* 2.7 25.3 + - - +
395C PRO* 4.0 22.7 - - + -
424C LYS* 3.7 41.3 - - + +
78D LYS 4.7 4.7 - - - -
79D ASN* 2.3 41.7 + - - -
80D SER* 3.7 6.8 - - - -
81D PRO* 3.5 24.0 - - + -
82D PRO* 1.3 74.9 - - - +
84D ILE* 1.3 54.1 + - - +
85D LEU* 2.6 20.7 + - + +
86D ASP* 2.9 25.8 + - + +
87D LEU* 3.1 17.6 + - + +
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Residues in contact with ILE 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D VAL* 4.5 4.0 - - + -
67D VAL* 5.1 2.4 - - - +
70D CYS* 4.0 31.6 - - + -
77D LEU* 4.4 25.1 - - + -
82D PRO 3.7 3.8 + - - -
83D TYR* 1.3 71.9 - - - +
85D LEU* 1.3 61.9 + - - +
86D ASP 3.5 0.5 + - - -
87D LEU* 4.0 9.8 - - - +
88D LEU* 3.7 41.4 + - + +
89D PRO* 4.4 0.2 - - - +
129D THR* 5.5 0.2 - - + -
151D LEU* 5.0 9.9 - - + -
155D SER* 3.3 25.6 + - - +
158D PHE* 3.3 39.3 - - + -
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D VAL* 3.7 33.5 - - + +
70D CYS* 4.0 17.5 - - + +
71D GLN* 4.0 18.8 - - + +
77D LEU* 3.1 35.7 - - + -
83D TYR* 2.6 10.3 + - + -
84D ILE* 1.3 77.3 - - + +
86D ASP* 1.3 65.3 + - - +
89D PRO* 2.9 21.6 - - - +
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Residues in contact with ASP 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C PRO* 6.0 0.9 - - - +
424C LYS* 3.0 33.8 + - - +
83D TYR* 2.9 15.7 + - + +
85D LEU* 1.3 82.7 - - - +
87D LEU* 1.3 61.8 + - + +
88D LEU 3.3 2.5 - - - -
89D PRO* 3.4 7.4 - - - +
90D ASP* 2.8 47.0 + - - +
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Residues in contact with LEU 87 (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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82D PRO* 3.3 33.2 - - + -
83D TYR* 3.1 22.9 + - + +
84D ILE* 3.8 8.0 + - - +
86D ASP* 1.3 80.1 - - + +
88D LEU* 1.3 53.9 + - + +
90D ASP* 4.6 0.7 - - - +
91D THR* 2.3 40.6 + - - +
155D SER 3.8 7.2 - - - +
158D PHE* 4.4 11.0 - - + +
159D SER* 3.8 28.9 - - - +
162D LEU* 3.7 26.3 - - + +
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Residues in contact with LEU 88 (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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63D MET* 3.2 35.8 - - + +
66D VAL* 3.7 33.7 - - + -
67D VAL* 3.8 19.3 - - + -
84D ILE* 3.7 28.1 + - + +
87D LEU* 1.3 79.2 - - + +
89D PRO* 1.3 69.6 - - + +
91D THR* 4.0 5.6 - - - +
92D TYR* 2.8 31.0 + - - +
122D LEU* 5.0 1.8 - - + -
126D THR* 5.7 0.4 - - - +
158D PHE* 3.9 33.7 - - + -
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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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67D VAL* 4.3 13.7 - - + -
85D LEU 2.9 29.8 - - - +
86D ASP* 3.4 10.8 - - - +
88D LEU* 1.3 92.7 - - + +
90D ASP* 1.3 63.4 + - - +
92D TYR* 3.1 9.0 + - + +
93D GLN* 2.9 36.2 + - + +
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Residues in contact with ASP 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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86D ASP* 2.8 33.5 + - - +
87D LEU* 6.0 0.3 - - - +
89D PRO* 1.3 76.1 - - - +
91D THR* 1.3 65.0 + - - +
93D GLN* 3.8 10.6 - - - +
94D HIS* 3.1 24.6 + - - +
162D LEU* 3.7 20.7 - - + +
166D LYS* 4.5 12.9 + - - +
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Residues in contact with THR 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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63D MET* 3.8 20.6 - - + -
87D LEU* 2.3 35.2 + - - +
88D LEU* 4.0 5.0 - - + +
90D ASP* 1.3 72.5 - - - +
92D TYR* 1.3 63.2 + - - +
94D HIS* 3.6 1.7 + - - +
95D LEU* 3.3 33.8 + - + +
118D PHE* 4.5 13.7 - - + -
122D LEU* 4.3 14.6 - - + -
158D PHE* 4.8 4.4 + - + +
161D MET* 6.0 1.8 - - + -
162D LEU* 3.9 27.6 + - + +
165D LEU* 4.6 4.8 - - + +
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Residues in contact with TYR 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D TRP* 3.1 61.1 - + + +
63D MET* 3.8 10.5 - - + +
88D LEU 2.8 19.1 + - - +
89D PRO* 3.1 9.6 + - + +
91D THR* 1.3 77.3 - - - +
93D GLN* 1.3 74.6 + - - +
95D LEU* 3.3 4.6 + - - +
96D ARG* 2.5 66.1 + - - +
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Residues in contact with GLN 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* 2.9 25.4 + - + +
90D ASP* 3.8 10.5 - - - +
91D THR 3.3 0.2 - - - -
92D TYR* 1.3 89.1 - - - +
94D HIS* 1.3 57.5 + - - +
96D ARG* 2.8 19.9 + - - +
97D THR* 2.8 32.5 + - - +
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Residues in contact with HIS 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ASP 3.1 17.0 + - - +
91D THR 4.1 3.8 - - - +
93D GLN* 1.3 76.2 - - - +
95D LEU* 1.3 57.0 + - - +
97D THR* 3.8 10.2 - - + -
98D ILE* 3.2 36.1 + - + +
162D LEU* 4.6 6.1 - - + -
165D LEU* 3.7 20.6 + - + -
166D LYS* 3.4 37.8 - - + +
169D PHE 2.7 30.1 + - - -
171D SER* 4.2 13.7 - - - -
172D GLY 3.9 5.3 + - - -
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Residues in contact with LEU 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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56D VAL* 5.6 2.2 - - + -
60D TRP* 4.4 24.0 - - + +
63D MET* 5.0 0.7 - - - -
91D THR* 3.3 22.8 + - + +
92D TYR* 3.3 7.3 + - - +
93D GLN 3.0 0.8 - - - -
94D HIS* 1.3 75.6 - - - +
96D ARG* 1.3 62.2 + - - +
97D THR 3.2 0.4 - - - -
98D ILE* 3.2 5.5 + - + +
99D LEU* 3.0 35.8 + - + +
115D PHE* 3.6 33.0 - - + -
118D PHE* 4.3 4.5 - - + -
119D MET* 4.1 12.6 - - + -
122D LEU* 3.7 29.6 - - + -
165D LEU* 3.6 22.2 - - + -
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Residues in contact with ARG 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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60D TRP* 3.9 21.6 - - + -
92D TYR* 2.5 58.8 + - + +
93D GLN* 2.8 20.5 + - - +
95D LEU* 1.3 75.1 - - - +
97D THR* 1.3 59.4 + - - +
99D LEU* 3.9 8.4 - - + +
100D SER* 2.9 27.7 + - - -
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Residues in contact with THR 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 GLN* 2.8 17.9 + - - +
94D HIS* 3.8 11.5 - - + -
96D ARG* 1.3 77.3 - - - +
98D ILE* 1.3 64.8 + - - +
100D SER* 3.3 14.3 + - - -
101D ARG* 3.4 20.1 + - - +
171D SER* 3.9 14.4 - - - +
172D GLY* 3.9 18.6 - - - +
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Residues in contact with ILE 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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94D HIS* 3.2 32.9 + - + +
95D LEU* 3.2 16.3 + - + +
97D THR* 1.3 77.4 - - - +
99D LEU* 1.3 62.7 + - + +
101D ARG* 3.2 5.5 + - - +
102D TYR* 3.1 28.4 - - + -
109D LEU* 4.1 20.9 - - + -
115D PHE* 4.2 15.7 - - + -
165D LEU* 4.1 13.0 - - + -
169D PHE* 3.5 41.3 - - + -
172D GLY* 3.6 28.3 - - - +
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Residues in contact with LEU 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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53D LYS* 3.9 29.8 - - + +
56D VAL* 4.2 16.2 - - + -
60D TRP* 4.0 23.8 - - + -
95D LEU 3.0 19.2 + - - +
96D ARG* 3.9 7.6 - - + +
98D ILE* 1.3 76.7 - - + +
100D SER* 1.3 61.1 + - - +
101D ARG 3.0 5.4 - - - -
102D TYR* 3.0 12.7 + - - +
103D GLU* 3.1 10.8 - - - +
106D MET* 3.2 26.0 - - + +
109D LEU* 3.7 25.1 - - + -
115D PHE* 4.5 11.2 - - + -
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Residues in contact with SER 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 ARG 2.9 19.4 + - - -
97D THR* 3.5 11.4 - - - -
98D ILE 3.2 0.4 - - - -
99D LEU* 1.3 76.4 - - - +
101D ARG* 1.3 59.6 + - - +
102D TYR 3.4 0.2 - - - -
103D GLU* 3.2 30.0 + - - +
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Residues in contact with ARG 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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359C ASP* 5.9 1.2 - - - +
360C HIS* 4.8 14.8 + - - -
362C LYS* 4.7 19.1 - - - +
97D THR* 3.4 14.8 - - + +
98D ILE 3.2 8.6 + - - +
99D LEU 3.0 1.2 - - - -
100D SER* 1.3 81.8 - - - +
102D TYR* 1.3 66.9 + - + +
103D GLU* 3.6 3.7 + - - -
105D LYS* 3.7 17.7 + - - -
171D SER* 3.1 30.6 + - - -
172D GLY* 4.0 16.8 - - - +
173D LEU* 4.4 21.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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