Contacts of the helix formed by residues 93 - 113 (chain B) in PDB entry 1YYV
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 THR 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLY 2.4 33.7 + - - +
75B PHE 3.0 5.5 + - - -
76B LEU 3.6 18.4 - - - +
77B ASN* 3.5 30.5 - - - +
92B LEU* 1.3 77.8 - - - +
94B PRO* 1.4 69.4 - - + +
95B LEU* 3.5 4.7 + - - +
96B GLY 3.1 12.8 + - - -
97B GLU* 2.9 25.7 + - - +
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Residues in contact with PRO 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 5.6 0.9 - - - +
92B LEU 4.7 0.2 - - - +
93B THR* 1.4 85.9 - - - +
95B LEU* 1.3 60.3 + - - +
97B GLU* 3.3 21.0 + - - +
98B GLN* 3.2 31.1 + - - +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TRP* 3.7 26.0 - - + -
113A ASN* 4.2 10.8 - - + +
116A GLN* 3.6 46.9 - - + +
117A VAL* 4.1 16.2 - - + +
120A GLN* 5.3 2.7 - - - +
73B ASP 4.2 5.8 - - - +
74B GLY* 3.9 12.8 - - - +
75B PHE* 4.0 22.2 - - + -
93B THR* 3.2 9.1 + - - +
94B PRO* 1.3 80.4 - - - +
96B GLY* 1.3 56.3 + - - +
98B GLN* 3.2 16.9 + - - +
99B VAL 3.2 21.5 + - - -
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Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.5 0.3 - - - +
75B PHE* 3.4 37.2 - - - +
92B LEU* 3.9 9.6 - - - +
93B THR* 3.1 11.8 + - - -
95B LEU* 1.3 72.2 - - - +
97B GLU* 1.3 53.3 + - - +
98B GLN 3.2 0.2 - - - -
99B VAL* 3.7 3.1 - - - +
100B SER* 2.8 38.9 + - - -
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 4.1 1.5 + - - +
92B LEU* 3.7 27.4 - - + +
93B THR 2.9 20.7 + - - +
94B PRO* 3.4 17.6 - - - +
96B GLY* 1.3 76.8 - - - +
98B GLN* 1.3 61.4 + - + +
100B SER* 3.6 5.4 - - - -
101B ASP* 3.2 30.0 + - - +
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Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TRP* 3.5 33.7 + - + +
113A ASN* 4.3 8.0 + - - +
94B PRO* 3.2 24.8 + - - +
95B LEU* 3.2 17.0 + - - +
96B GLY 3.2 0.6 - - - -
97B GLU* 1.3 76.7 - - + +
99B VAL* 1.3 65.5 + - - +
101B ASP* 3.5 19.1 + - - +
102B MLY 3.7 12.3 - - - +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 3.9 20.2 - - + -
109A TRP* 3.6 36.9 - - + -
110A ILE* 4.6 1.8 - - + -
29B VAL* 4.1 19.5 - - + -
38B LEU* 4.1 16.2 - - + -
75B PHE* 3.7 33.0 - - + -
95B LEU 3.2 5.7 + - - -
96B GLY* 3.7 7.6 - - - +
98B GLN* 1.3 76.4 - - - +
100B SER* 1.3 55.2 + - - +
102B MLY 3.0 7.7 + - - +
103B VAL* 2.8 33.2 + - + +
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.0 33.7 + - - -
39B VAL* 5.3 0.5 - - - +
42B ARG* 3.0 22.2 + - - +
92B LEU* 3.9 7.9 - - - -
96B GLY 2.8 22.4 + - - -
97B GLU 3.6 5.2 - - - -
99B VAL* 1.3 78.5 - - - +
101B ASP* 1.3 52.4 + - - +
103B VAL* 3.8 7.2 - - - +
104B ALA* 2.7 37.9 + - - +
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG* 2.5 43.1 + - - +
97B GLU* 3.2 15.6 + - - +
98B GLN* 3.6 12.2 - - - +
100B SER* 1.3 74.6 - - - +
102B MLY 1.3 65.8 + - + +
104B ALA* 4.2 1.1 - - - +
105B ALA* 3.1 27.4 + - - +
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Residues in contact with MLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A MLY 4.8 3.3 - - - +
105A ALA* 4.1 29.2 - - + -
106A LEU* 3.7 27.6 - - + +
109A TRP* 3.9 40.6 - - + -
98B GLN 3.7 13.7 - - - +
99B VAL* 3.0 6.6 + - - +
101B ASP* 1.3 80.0 + - + +
103B VAL* 1.4 67.2 + - - +
105B ALA* 3.6 5.8 + - + +
106B LEU* 3.3 21.7 + - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 3.6 25.4 - - + -
29B VAL* 3.6 24.2 - - + +
30B THR* 5.4 0.2 - - - +
35B VAL* 4.0 45.5 - - + +
38B LEU* 4.1 14.6 - - + -
39B VAL* 4.5 2.5 - - + -
99B VAL 2.8 19.4 + - - +
100B SER* 3.8 7.0 - - - +
102B MLY 1.4 77.8 + - - +
104B ALA* 1.3 57.5 + - - +
106B LEU* 3.2 10.8 + - + +
107B ALA* 2.9 24.1 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.9 19.5 - - + +
42B ARG* 3.6 33.2 - - - +
100B SER 2.7 21.4 + - - +
101B ASP 4.2 1.6 - - - +
103B VAL* 1.3 70.4 - - - +
105B ALA* 1.3 59.6 + - - +
107B ALA* 3.7 1.2 - - - +
108B ASP* 2.8 34.1 + - - +
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A MLY 4.0 32.8 - - + -
101B ASP 3.1 19.7 + - - +
102B MLY 3.9 7.0 - - + +
103B VAL 3.4 0.2 - - - -
104B ALA* 1.3 75.8 - - - +
106B LEU* 1.3 56.6 + - - +
108B ASP* 3.9 4.4 - - - +
109B TRP* 3.0 28.9 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.6 8.5 - - + -
29A VAL* 4.3 0.7 - - + -
30A THR* 3.6 30.7 - - + -
99A VAL* 4.1 10.1 - - + -
102A MLY 3.7 32.9 - - + +
103A VAL* 4.0 19.5 - - + -
106A LEU* 4.3 17.7 - - + -
30B THR* 4.8 1.1 - - - +
102B MLY 3.3 10.1 + - - +
103B VAL* 3.2 11.1 + - + +
104B ALA 3.2 0.4 - - - -
105B ALA* 1.3 77.3 - - - +
107B ALA* 1.3 64.9 + - - +
109B TRP* 3.3 1.7 + - + +
110B ILE* 3.0 43.9 + - + +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.6 24.9 - - + +
26A LEU* 5.6 1.8 - - - +
35B VAL* 4.1 16.8 - - + -
39B VAL* 4.2 9.6 - - + -
103B VAL 2.9 15.0 + - - +
104B ALA* 3.7 9.4 - - - +
106B LEU* 1.3 77.8 - - - +
108B ASP* 1.3 60.9 + - - +
110B ILE* 3.4 5.5 + - - +
111B GLU* 3.0 30.3 + - - +
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Residues in contact with ASP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ALA 2.8 21.6 + - - +
105B ALA* 4.1 4.7 - - - +
107B ALA* 1.3 71.2 - - - +
109B TRP* 1.3 65.3 + - - +
111B GLU* 3.9 13.9 - - - +
112B LEU* 2.9 37.7 + - - +
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Residues in contact with TRP 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 5.4 0.4 - - + -
75A PHE* 3.8 20.6 - + - -
95A LEU* 3.6 19.1 - - + -
98A GLN* 3.1 46.0 + - + +
99A VAL* 3.5 37.9 - - + -
102A MLY 4.1 35.9 - - + -
105B ALA 3.0 19.2 + - - +
106B LEU* 3.8 4.3 - - + +
108B ASP* 1.3 76.7 + - - +
110B ILE* 1.3 72.9 + - + +
112B LEU* 4.5 5.4 - - + -
113B ASN* 2.8 68.5 + - + +
117B VAL* 5.2 3.6 - - + -
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 5.0 3.4 - - + -
22A SER* 3.6 34.5 - - - +
25A VAL* 4.0 23.1 - - + +
26A LEU* 3.9 32.5 - - + +
29A VAL* 3.9 9.4 - - + -
99A VAL* 4.7 0.4 - - + -
106B LEU* 3.0 44.1 + - + +
107B ALA* 3.7 4.9 - - - +
109B TRP* 1.3 93.9 - - + +
111B GLU* 1.3 64.0 + - - +
113B ASN 3.7 0.9 - - - -
114B LEU* 3.0 23.1 + - + +
117B VAL* 6.0 0.3 - - - +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.4 8.7 - - + -
13A GLY* 2.8 53.1 + - - +
14A ASN* 3.5 6.8 - - - +
15A LEU* 3.0 42.7 + - + +
16A PHE* 4.8 5.7 + - - -
22A SER* 4.5 2.0 - - - +
107B ALA* 3.0 23.1 + - - +
108B ASP* 3.9 15.7 - - - +
110B ILE* 1.3 76.0 - - - +
112B LEU* 1.3 63.1 + - - +
114B LEU* 3.4 7.2 + - - -
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.7 35.0 + - - +
108B ASP* 2.9 31.1 + - - +
109B TRP* 3.8 7.2 - - + +
111B GLU* 1.3 77.4 - - - +
113B ASN* 1.3 71.9 + - - +
114B LEU 3.3 0.2 - - - -
115B PRO* 3.5 13.5 - - - +
116B GLN* 4.2 4.3 - - - +
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Residues in contact with ASN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.9 8.8 - - + +
98A GLN* 4.1 7.4 + - - +
109B TRP* 2.8 76.6 + - + +
110B ILE 3.7 2.0 - - - -
112B LEU* 1.3 86.8 - - - +
114B LEU* 1.3 66.7 + - - +
115B PRO* 3.3 2.7 - - - -
116B GLN* 2.5 41.5 + - - +
117B VAL* 3.3 13.4 + - - +
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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