Contacts of the helix formed by residues 83 - 102 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78F LYS 4.1 7.4 - - - -
79F ASN* 3.6 26.0 + - + +
80F SER* 3.7 12.2 + - - -
81F PRO* 3.3 37.5 - - + +
82F PRO* 1.3 73.2 - - - +
84F ILE* 1.3 58.6 + - - +
85F LEU* 3.2 3.6 - - + +
86F ASP* 2.9 39.7 + - + +
87F LEU* 3.0 18.2 + - + +
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Residues in contact with ILE 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F VAL* 4.2 9.6 - - + -
70F CYS* 4.4 21.8 - - + -
77F LEU* 4.7 15.5 - - + -
82F PRO 3.9 2.2 - - - -
83F TYR* 1.3 72.2 - - - +
85F LEU* 1.3 60.2 + - + +
86F ASP 3.2 0.2 - - - -
87F LEU* 3.7 11.0 - - + -
88F LEU* 3.2 45.8 + - + +
151F LEU* 5.0 10.8 - - + -
155F SER* 3.4 30.3 - - - +
158F PHE* 3.4 38.4 - - + -
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F VAL* 3.2 38.4 - - + +
70F CYS* 3.7 30.3 - - + +
71F GLN* 3.6 27.8 - - + +
77F LEU* 5.4 8.3 - - + -
83F TYR* 3.2 1.4 + - + -
84F ILE* 1.3 79.3 - - + +
86F ASP* 1.3 57.4 + - - +
88F LEU* 5.3 1.3 - - + -
89F PRO* 2.7 30.3 - - - +
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Residues in contact with ASP 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F TYR* 2.9 31.7 + - + +
85F LEU* 1.3 81.7 - - - +
87F LEU* 1.3 69.4 + - + +
89F PRO* 3.0 12.4 - - - +
90F ASP* 3.1 31.5 + - - +
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Residues in contact with LEU 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F PRO* 3.7 15.3 - - + -
83F TYR* 3.0 23.0 + - + +
84F ILE* 3.5 10.2 + - + -
86F ASP* 1.3 82.0 - - + +
88F LEU* 1.3 53.3 + - - +
90F ASP* 3.6 5.9 + - - +
91F THR* 2.5 39.0 + - - +
155F SER 3.5 13.0 - - - +
158F PHE* 3.9 15.0 - - + +
159F SER* 3.2 44.4 - - - +
162F LEU* 4.3 14.1 - - + +
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Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F MET* 2.8 50.3 - - + +
66F VAL* 3.6 22.4 - - + +
67F VAL* 3.3 33.7 - - + +
70F CYS* 5.4 0.2 - - - -
84F ILE* 3.2 30.8 + - + +
87F LEU* 1.3 71.9 - - + +
89F PRO* 1.3 72.4 - - + +
91F THR* 3.5 2.8 + - + +
92F TYR* 3.2 9.7 + - - +
122F LEU* 6.0 1.3 - - + -
126F THR* 5.3 1.3 - - - +
158F PHE* 4.0 36.8 - - + -
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Residues in contact with PRO 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F VAL* 4.8 7.4 - - + -
85F LEU* 2.7 31.2 - - - +
86F ASP* 3.0 9.6 - - - +
88F LEU* 1.3 93.0 - - + +
90F ASP* 1.3 59.4 + - - +
92F TYR* 2.9 10.7 + - + +
93F GLN* 2.8 37.3 + - - +
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Residues in contact with ASP 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ASP* 3.1 28.3 + - - +
87F LEU* 3.9 1.8 - - - +
89F PRO* 1.3 81.3 - - - +
91F THR* 1.3 55.1 + - - +
93F GLN* 3.0 43.4 + - - +
94F HIS* 3.1 15.4 + - - +
162F LEU* 3.8 26.0 - - + +
166F LYS* 5.6 4.1 + - - -
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Residues in contact with THR 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F MET* 4.2 11.2 - - + -
87F LEU* 2.5 25.0 + - - +
88F LEU* 3.7 8.6 - - - +
89F PRO 3.1 0.4 - - - -
90F ASP* 1.3 74.6 - - - +
92F TYR* 1.3 63.4 + - - +
94F HIS* 4.0 1.0 - - - +
95F LEU* 3.3 36.3 + - + +
118F PHE* 4.5 14.4 - - + -
122F LEU* 4.5 16.4 - - + -
158F PHE* 5.1 6.0 + - + +
161F MET* 6.2 1.1 - - + -
162F LEU* 3.6 27.4 - - + +
165F LEU* 4.7 2.1 - - + +
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Residues in contact with TYR 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F TRP* 3.2 57.9 - + + +
63F MET* 4.2 9.2 - - + -
88F LEU 3.2 13.1 + - - +
89F PRO* 2.9 12.0 + - + +
91F THR* 1.3 77.7 - - - +
93F GLN* 1.3 70.9 + - + +
95F LEU* 3.0 6.4 + - - +
96F ARG* 2.6 64.4 + - - +
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Residues in contact with GLN 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F PRO 2.8 10.2 + - - +
90F ASP* 3.0 42.6 + - - +
92F TYR* 1.3 83.9 - - + +
94F HIS* 1.3 64.6 + - - +
96F ARG* 3.2 8.4 + - - +
97F THR* 2.9 31.9 + - - +
166F LYS* 5.6 6.7 - - - +
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Residues in contact with HIS 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ASP 3.1 15.4 + - - +
91F THR 4.4 2.5 - - - +
92F TYR 3.1 0.6 - - - -
93F GLN* 1.3 83.8 - - + +
95F LEU* 1.3 59.5 + - - +
96F ARG 3.1 2.0 - - - -
97F THR* 3.4 11.8 - - + +
98F ILE* 2.9 44.9 + - + +
162F LEU* 4.7 4.0 - - + -
165F LEU* 3.8 17.9 + - + -
166F LYS* 3.9 35.1 - - + +
169F PHE* 2.8 31.9 + - - +
170F PRO* 4.8 0.2 - - + -
171F SER* 4.5 5.8 - - - -
172F GLY* 3.9 8.9 + - - -
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F VAL* 5.2 2.5 - - + -
60F TRP* 4.1 24.7 - - + +
63F MET* 5.2 0.9 - - - -
91F THR* 3.3 25.0 + - + +
92F TYR* 3.0 5.0 + - - +
94F HIS* 1.3 77.8 - - - +
96F ARG* 1.3 58.3 + - - +
98F ILE* 3.6 9.4 + - + +
99F LEU* 3.1 32.3 + - + +
115F PHE* 3.5 33.9 - - + -
118F PHE* 4.5 4.0 - - + -
119F MET* 3.9 11.0 - - + -
122F LEU* 3.4 32.8 - - + -
165F LEU* 4.2 17.7 - - + -
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Residues in contact with ARG 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LYS* 6.0 2.8 - - - +
60F TRP* 3.3 36.3 - - + -
92F TYR* 2.6 64.0 + - + +
93F GLN* 3.5 9.9 - - - +
95F LEU* 1.3 75.3 - - - +
97F THR* 1.3 65.3 + - - +
98F ILE 2.9 1.3 - - - -
99F LEU* 2.9 7.1 + - - +
100F SER* 2.8 27.9 + - - -
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Residues in contact with THR 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F GLN* 2.9 17.7 + - - +
94F HIS* 3.4 17.6 - - + +
96F ARG* 1.3 74.6 - - - +
98F ILE* 1.3 60.3 + - - +
100F SER* 3.3 10.5 + - - +
101F ARG* 3.2 24.3 - - + +
171F SER* 4.1 9.0 - - - +
172F GLY* 4.0 21.8 - - - +
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Residues in contact with ILE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F HIS* 2.9 36.3 + - + +
95F LEU* 3.8 17.0 - - + +
96F ARG 2.9 0.8 - - - -
97F THR* 1.3 74.8 - - - +
99F LEU* 1.3 65.3 + - + +
101F ARG* 3.2 10.9 + - - +
102F TYR* 3.2 19.0 + - + -
109F LEU* 4.2 22.0 - - + -
115F PHE* 4.5 10.5 - - + -
165F LEU* 4.2 13.2 - - + -
169F PHE* 3.5 41.1 - - + -
172F GLY* 3.4 24.7 - - - -
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Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LYS* 4.0 30.9 + - + +
56F VAL* 4.1 16.6 - - + -
60F TRP* 3.5 33.7 - - + -
95F LEU 3.1 20.1 + - - +
96F ARG* 2.9 8.8 + - - +
98F ILE* 1.3 75.0 - - + +
100F SER* 1.3 66.1 + - - +
102F TYR* 3.8 5.5 - - - +
103F GLU* 3.5 20.6 + - - +
106F MET* 3.3 39.3 - - + +
109F LEU* 4.1 12.6 - - + -
115F PHE* 5.4 6.1 - - + -
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Residues in contact with SER 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F ARG 2.8 13.1 + - - -
97F THR* 3.3 14.4 + - - -
99F LEU* 1.3 78.4 - - - +
101F ARG* 1.3 65.1 + - - +
102F TYR 3.1 0.2 - - - -
103F GLU* 2.7 38.5 - - - +
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Residues in contact with ARG 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F THR* 3.2 20.0 + - + +
98F ILE 3.2 10.1 + - - +
100F SER* 1.3 84.5 + - - +
102F TYR* 1.3 59.2 + - + +
103F GLU 3.5 0.8 + - - -
105F LYS* 3.4 19.8 + - - -
171F SER* 3.0 34.6 + - - +
172F GLY 3.6 12.8 - - - +
173F LEU* 4.4 16.6 - - + +
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Residues in contact with TYR 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F ILE* 3.2 26.8 + - + +
99F LEU 3.5 5.1 + - - +
100F SER 3.1 0.8 - - - -
101F ARG* 1.3 80.5 - - - +
103F GLU* 1.3 53.9 - - - +
105F LYS* 2.9 39.3 + - + -
106F MET* 2.7 36.3 + - - +
108F THR* 4.0 15.9 - - - -
109F LEU* 4.3 32.3 - - + -
169F PHE* 4.1 10.8 - + - -
172F GLY 3.5 18.4 - - - -
173F LEU* 4.0 22.5 - - + +
174F PHE* 3.0 35.7 + - + +
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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