Contacts of the helix formed by residues 99 - 111 (chain B) in PDB entry 5UQ3
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 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A VAL* 3.7 22.2 - - + -
155A PRO* 3.7 29.4 - - + +
156A VAL* 5.2 4.9 - - + -
157A ARG* 4.1 7.9 - - - +
97B ASP* 3.0 22.8 + - - +
98B LYS* 1.3 110.3 + - + +
100B LEU* 1.3 53.9 + - + +
101B LEU 3.1 1.3 - - - -
102B ALA* 2.9 7.0 + - - +
103B MET* 2.8 40.2 + - - +
179B ARG* 3.8 10.5 + - + -
182B CYS* 3.5 31.0 - - + -
183B GLU* 3.0 35.8 + - + +
186B MET* 5.0 1.1 - - + -
198B GLU* 6.5 0.2 - - + -
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Residues in contact with LEU 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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157A ARG* 3.7 15.0 - - - +
94B LYS 4.0 0.4 - - - +
95B ILE 3.2 23.1 - - - +
97B ASP* 3.1 25.2 + - + +
99B TYR* 1.3 76.9 - - - +
101B LEU* 1.3 59.2 + - - +
103B MET* 3.4 25.5 + - - +
104B THR* 2.9 27.9 + - - -
127B LEU* 3.9 16.9 - - + +
130B ALA* 4.0 23.7 - - + +
131B ASN* 3.8 13.0 - - - +
134B GLU* 4.3 3.8 - - + -
135B GLU* 3.7 19.7 - - + +
199B ARG* 3.8 6.3 - - - +
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Residues in contact with LEU 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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74B PHE* 3.2 17.8 - - - -
78B PHE* 4.2 15.5 - - + -
87B LEU* 4.0 17.0 - - + -
96B ALA* 3.8 27.6 - - + +
97B ASP 2.9 21.5 + - - +
98B LYS* 4.1 1.8 - - - +
100B LEU* 1.3 74.5 - - - +
102B ALA* 1.3 61.2 + - - +
104B THR* 3.1 17.9 - - - +
123B PHE* 3.5 35.7 - - + -
127B LEU* 4.0 7.4 - - + -
194B ILE* 3.6 34.1 - - + -
195B TRP* 5.4 2.6 + - - -
197B ARG* 4.9 4.7 - - - +
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Residues in contact with ALA 102 (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 PHE* 5.7 0.7 - - - -
98B LYS 3.3 14.3 + - - +
99B TYR* 2.9 11.1 + - - +
101B LEU* 1.3 76.5 - - - +
103B MET* 1.3 60.5 + - - +
104B THR 3.2 0.2 - - - -
105B PHE* 3.0 9.8 + - - +
106B VAL* 2.9 30.3 + - - +
182B CYS* 3.9 9.9 - - - +
185B VAL* 3.6 25.3 - - + +
186B MET* 3.8 14.1 - - + -
195B TRP* 5.0 4.5 - - - +
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Residues in contact with MET 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A VAL* 4.9 5.6 - - - -
99B TYR* 2.8 21.2 + - - +
100B LEU* 3.7 27.6 - - - +
102B ALA* 1.3 77.3 - - - +
104B THR* 1.3 57.8 + - - +
106B VAL* 3.1 10.4 + - - +
107B TYR* 2.9 58.6 + - + +
130B ALA* 3.9 20.6 - - + +
133B VAL* 5.0 2.0 - - + -
134B GLU* 3.9 28.5 - - + +
175B ALA 4.2 6.5 - - - +
177B VAL* 4.3 13.7 - - + +
182B CYS* 3.7 22.9 - - - -
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Residues in contact with THR 104 (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 PHE* 3.8 11.2 - - + -
100B LEU 2.9 13.6 + - - -
101B LEU* 3.1 28.3 - - - +
103B MET* 1.3 75.5 - - - +
105B PHE* 1.3 57.4 + - - +
107B TYR* 3.9 5.4 - - - +
108B PHE* 3.2 30.2 + - - -
123B PHE* 3.4 39.9 + - + -
126B ALA* 3.1 28.9 - - - +
127B LEU* 3.4 10.4 + - - -
130B ALA* 4.9 0.4 - - - +
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Residues in contact with PHE 105 (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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67B GLN* 6.5 0.4 - - + -
68B ARG* 5.6 4.3 - - + -
71B MET* 3.6 42.0 - - + -
74B PHE* 3.6 49.4 - + + -
101B LEU 4.0 1.8 - - - +
102B ALA* 3.0 10.0 + - - +
104B THR* 1.3 78.7 - - - +
106B VAL* 1.3 65.2 + - - +
107B TYR 3.1 1.6 - - - -
108B PHE* 2.8 26.7 + - + +
109B LYS* 2.9 23.1 + - + +
118B HIS* 6.3 1.6 - + - -
185B VAL* 3.9 33.7 - - + -
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Residues in contact with VAL 106 (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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67B GLN* 5.9 4.5 - - - +
102B ALA 2.9 22.5 + - - +
103B MET* 3.1 7.2 + - - +
105B PHE* 1.3 77.7 - - + +
107B TYR* 1.3 57.1 + - - +
109B LYS* 3.2 8.3 + - + +
110B ARG* 2.9 51.6 + - + +
177B VAL* 3.8 40.4 - - + -
181B CYS* 4.8 10.1 - - - +
182B CYS* 5.4 1.1 - - - -
185B VAL* 4.3 23.6 - - + -
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Residues in contact with TYR 107 (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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103B MET* 2.9 34.3 + - + +
104B THR* 3.9 6.5 - - - +
105B PHE 3.1 0.2 - - - -
106B VAL* 1.3 77.1 - - - +
108B PHE* 1.3 60.8 + - + +
110B ARG* 4.3 9.2 - - + -
111B ALA* 3.0 31.9 + - - +
126B ALA* 3.7 27.6 - - + -
129B LEU* 4.0 13.5 - - + -
130B ALA* 3.7 33.4 + - + -
133B VAL* 4.4 1.9 - - - +
167B LEU* 4.7 6.3 - - + +
171B ILE* 3.6 20.8 - - + +
174B ARG 4.2 1.8 - - - -
175B ALA* 2.4 54.4 + - + +
177B VAL* 3.9 11.2 - - + -
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Residues in contact with PHE 108 (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 PHE* 3.6 33.2 - + + -
77B LEU* 3.8 13.5 - - + -
104B THR 3.2 14.8 - - - -
105B PHE* 2.8 17.0 + - + +
107B TYR* 1.3 77.9 - - - +
109B LYS* 1.3 62.9 + - - +
111B ALA 3.6 0.7 + - - -
112B LYS 3.2 14.7 + - - -
113B PHE* 3.2 38.8 + + + +
118B HIS* 3.3 37.9 - + + +
119B THR 5.1 0.4 - - - -
122B ASN* 3.0 32.3 - - + -
123B PHE* 3.6 19.7 - + + -
126B ALA* 4.1 7.9 - - + -
167B LEU* 5.8 0.7 - - + -
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Residues in contact with LYS 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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67B GLN* 4.5 33.0 - - + +
68B ARG* 5.8 9.4 - - + +
105B PHE* 2.9 24.0 + - + +
106B VAL* 3.6 11.4 - - + +
108B PHE* 1.3 77.4 - - - +
110B ARG* 1.3 60.3 + - + +
112B LYS* 2.8 53.3 + - + +
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Residues in contact with ARG 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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57A GLU* 5.6 2.4 + - - -
106B VAL* 2.9 38.9 + - + +
107B TYR* 4.3 5.5 - - - -
109B LYS* 1.3 81.1 - - + +
111B ALA* 1.3 60.3 + - - +
112B LYS* 3.2 4.4 + - - +
170B ARG 4.2 2.6 - - - +
171B ILE* 3.8 31.0 - - + +
174B ARG* 2.8 60.1 + - - +
176B ILE 3.5 20.2 + - - -
177B VAL* 4.1 15.8 - - - +
181B CYS* 5.5 4.6 - - - -
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Residues in contact with ALA 111 (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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107B TYR 3.0 18.2 + - - +
108B PHE 4.1 0.2 - - - +
110B ARG* 1.3 76.0 - - - +
112B LYS* 1.3 65.9 + - - +
113B PHE* 3.4 27.8 - - + -
167B LEU* 4.0 4.7 - - + -
170B ARG* 2.5 44.1 + - + +
171B ILE* 3.6 15.9 - - + -
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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