Contacts of the helix formed by residues 89 - 101 (chain B) in PDB entry 1YVP
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 GLN 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B SER* 3.6 26.7 + - - +
84B GLY* 6.0 1.2 - - - -
86B ALA* 4.8 6.2 - - - +
87B ALA 5.9 0.2 - - - +
88B LYS* 1.3 80.5 - - - +
90B GLU* 1.3 66.3 + - - +
91B PRO* 3.4 1.6 - - - -
92B THR* 3.0 22.4 + - - +
93B LEU* 2.7 46.3 + - + +
118B VAL* 3.8 11.5 + - - +
120B ARG* 3.8 18.1 + - - +
124B HIS* 3.4 28.2 + - + +
8H C 4.5 12.3 + - + +
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Residues in contact with GLU 90 (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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88B LYS* 3.7 19.3 + - + +
89B GLN* 1.3 82.1 + - - +
91B PRO* 1.3 70.5 - - + +
93B LEU* 3.1 4.1 + - - +
94B PHE* 2.8 27.2 + - - +
127B THR* 4.4 11.7 - - + -
131B PHE* 3.4 26.1 - - + -
5H G 4.8 10.0 + - - +
6H U 3.7 19.2 + - - +
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Residues in contact with PRO 91 (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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36B PHE* 3.0 49.6 - - + +
37B LEU* 3.8 15.7 - - - +
39B PHE 4.9 0.7 - - - -
40B GLY* 3.4 27.8 - - - +
88B LYS* 4.0 19.1 - - + +
89B GLN 3.5 3.4 - - - -
90B GLU* 1.3 93.1 - - + +
92B THR* 1.3 62.8 + - - +
94B PHE* 3.3 1.0 + - + +
95B ALA* 3.0 22.0 + - - +
386B LEU* 5.7 1.6 - - + -
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Residues in contact with THR 92 (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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37B LEU* 3.6 25.7 + - - +
77B ILE* 3.4 24.5 - - + +
80B PHE* 5.0 5.0 - - - +
81B SER* 4.3 14.0 + - - -
86B ALA* 4.7 6.4 - - - +
88B LYS 4.4 6.8 + - - -
89B GLN* 3.0 22.1 + - - +
91B PRO* 1.3 81.7 - - - +
93B LEU* 1.3 61.6 + - - +
95B ALA* 3.4 2.6 + - - +
96B LEU* 3.1 21.8 + - - +
118B VAL* 4.0 19.3 - - + -
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Residues in contact with LEU 93 (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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89B GLN* 2.7 44.4 + - + +
90B GLU* 3.8 3.6 - - + +
92B THR* 1.3 70.0 - - - +
94B PHE* 1.3 60.6 + - - +
96B LEU* 4.4 4.3 - - + -
97B ALA* 3.0 27.4 + - - +
118B VAL* 3.9 18.2 - - + -
119B CYS* 3.8 20.0 - - - -
124B HIS* 3.6 42.0 - - + +
127B THR* 3.8 28.3 - - + +
128B PHE* 3.8 13.7 - - + -
131B PHE* 3.8 4.3 - - + -
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Residues in contact with PHE 94 (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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36B PHE* 3.9 24.5 - + + -
54B GLY 5.4 2.0 - - - -
57B ASN 5.8 0.2 - - - -
58B ALA* 4.3 29.8 - - + -
61B LEU* 4.6 3.4 - - + -
90B GLU 2.8 20.9 + - - +
91B PRO* 3.6 5.2 - - + +
93B LEU* 1.3 75.1 - - - +
95B ALA* 1.3 58.4 + - - +
97B ALA* 3.1 4.9 + - - +
98B VAL* 2.9 47.2 + - + +
131B PHE* 3.5 39.0 - + + -
134B ASP* 6.2 2.0 - - + -
135B LEU* 4.0 24.7 - - + -
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Residues in contact with ALA 95 (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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33B LEU* 4.4 13.0 - - + -
36B PHE* 4.9 3.1 - - + -
37B LEU* 4.6 2.2 - - + -
61B LEU* 3.7 26.6 - - + +
77B ILE* 3.5 24.2 - - + -
91B PRO 3.0 17.0 + - - +
92B THR 3.7 2.0 - - - +
94B PHE* 1.3 74.9 - - - +
96B LEU* 1.3 64.1 + - - +
98B VAL* 3.5 1.9 + - - +
99B CYS* 3.1 29.3 + - - -
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Residues in contact with LEU 96 (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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74B VAL* 4.7 7.4 - - + -
77B ILE* 3.8 22.4 - - + +
92B THR 3.1 17.4 + - - +
93B LEU* 3.8 6.3 - - + +
95B ALA* 1.3 73.0 - - - +
97B ALA* 1.3 68.2 + - - +
99B CYS* 3.3 3.6 + - - +
100B SER* 2.9 24.3 + - - -
111B ALA* 3.8 25.9 - - + +
114B ALA* 4.1 14.1 - - + -
115B VAL* 4.1 18.4 - - + -
118B VAL* 4.0 27.4 - - + -
119B CYS* 4.7 3.8 - - - -
128B PHE* 3.7 22.2 - - + -
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Residues in contact with ALA 97 (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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93B LEU 3.0 15.4 + - - +
94B PHE 3.1 10.1 + - - +
96B LEU* 1.3 75.6 - - - +
98B VAL* 1.3 65.3 + - - +
100B SER* 2.5 26.9 + - - -
101B GLN* 3.4 8.8 + - - +
128B PHE* 3.5 9.8 - - + -
131B PHE* 3.8 15.3 - - + -
132B LYS* 3.8 15.4 - - + +
135B LEU* 3.7 17.3 - - + -
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Residues in contact with VAL 98 (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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58B ALA* 5.6 2.2 - - + +
61B LEU* 3.9 17.3 - - + -
62B LEU* 4.0 27.6 - - + -
65B ILE* 4.1 12.8 - - + -
94B PHE* 2.9 41.8 + - + +
95B ALA 3.7 7.0 - - - +
97B ALA* 1.3 75.6 - - - +
99B CYS* 1.3 64.0 + - - +
100B SER 3.1 0.3 + - - -
101B GLN 3.0 22.2 - - - +
103B SER* 3.3 4.3 + - - -
135B LEU* 3.7 24.0 - - + +
139B MET* 3.9 9.3 - - + +
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Residues in contact with CYS 99 (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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61B LEU* 4.2 3.4 - - - -
65B ILE* 4.1 15.7 - - - -
73B VAL* 3.7 30.1 - - - -
74B VAL* 4.0 13.0 - - + -
77B ILE* 4.5 1.8 - - - -
95B ALA 3.1 23.2 + - - +
96B LEU* 3.7 5.8 - - - +
97B ALA 3.3 0.2 - - - -
98B VAL* 1.3 78.1 - - - +
100B SER* 1.3 61.0 + - - +
101B GLN 3.4 0.3 + - - -
103B SER* 3.4 24.7 + - - -
107B THR* 3.8 13.6 - - + +
108B LYS* 3.4 14.9 + - - -
111B ALA* 3.9 11.4 - - + -
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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
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96B LEU 2.9 12.1 + - - -
97B ALA* 2.5 23.9 + - - -
99B CYS* 1.3 78.3 - - - +
101B GLN* 1.3 58.4 + - - +
108B LYS* 3.4 10.9 + - - +
111B ALA* 3.8 13.9 - - - +
112B PHE* 3.3 32.8 - - - -
128B PHE* 3.9 13.7 - - - -
132B LYS* 2.7 29.2 + - - +
5E G 4.9 1.6 + - - -
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Residues in contact with GLN 101 (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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97B ALA 3.9 8.5 - - - +
98B VAL 3.0 14.4 + - - +
99B CYS 3.3 1.0 - - - -
100B SER* 1.3 79.6 - - - +
102B CYS* 1.3 67.8 + - - +
103B SER 2.8 10.7 + - - -
108B LYS* 3.7 4.5 - - - +
132B LYS* 2.9 61.3 + - - +
135B LEU* 3.6 17.3 + - + +
136B LYS* 3.7 8.3 - - - +
139B MET* 3.2 16.6 - - - +
141B CYS* 3.1 29.7 - - - -
142B GLY 4.2 10.3 + - - +
143B MET* 4.0 4.0 - - - +
5E G 5.7 0.9 - - - +
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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
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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