Contacts of the helix formed by residues 108 - 118 (chain B) in PDB entry 5HRI
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 GLU 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ARG* 2.9 34.7 + - - -
104B ALA* 3.4 6.6 - - + +
105B LEU* 2.6 52.3 + - + +
107B GLU* 1.3 75.6 - - + +
109B LYS* 1.3 62.8 + - - -
110B PRO* 3.5 2.7 - - - -
111B TYR* 3.0 23.3 + - - +
112B ALA* 3.0 10.4 + - - +
139B GLN 3.9 9.8 - - - +
140B TYR* 3.5 35.8 - - + +
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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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32B LYS 4.5 13.3 + - - -
35B VAL* 4.7 7.5 - - - +
53B LEU* 4.6 0.2 - - - +
55B ILE* 3.7 40.3 - - + +
104B ALA* 4.7 0.9 - - - -
105B LEU 3.2 5.4 + - - +
106B ALA* 3.4 16.3 + - - +
108B GLU* 1.3 74.9 - - - +
110B PRO* 1.3 69.5 - - + +
112B ALA* 3.0 5.4 + - - +
113B ILE* 2.9 54.6 + - + +
154B THR 5.7 2.0 - - - +
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Residues in contact with PRO 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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106B ALA 4.5 4.0 - - - +
107B GLU 4.5 3.6 - - - +
108B GLU 3.6 1.8 - - - -
109B LYS* 1.3 97.0 - - + +
111B TYR* 1.3 64.4 + - + +
113B ILE* 4.1 6.2 - - + +
114B PHE* 3.1 27.9 + - - +
153B ILE* 3.7 24.2 - - + +
154B THR 3.6 20.0 - - - +
155B THR 3.7 25.8 - - - +
156B GLU* 3.9 11.9 - - - +
159B LEU* 3.7 8.2 - - + +
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Residues in contact with TYR 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 GLU 3.9 19.1 - - - -
108B GLU 3.0 12.0 + - - +
110B PRO* 1.3 88.8 - - + +
112B ALA* 1.3 57.6 + - - +
113B ILE 3.5 0.2 - - - -
114B PHE* 3.7 3.9 - - - +
115B HIS* 3.1 28.2 + - - +
137B LEU* 4.0 9.6 - - + -
138B ASN 3.8 5.4 - - - +
139B GLN* 3.5 22.2 - - - +
140B TYR 4.1 2.7 - - - -
141B GLY* 3.6 25.1 - - - -
142B LEU* 3.6 19.2 + - + -
148B LEU* 5.4 4.0 - - + +
149B VAL 4.2 7.4 + - - -
151B LEU* 3.4 28.9 + - - +
153B ILE* 3.9 7.4 - - + +
159B LEU* 3.5 34.1 - - + -
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Residues in contact with ALA 112 (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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53B LEU* 3.8 9.2 - - + -
104B ALA* 3.6 30.3 - - + -
108B GLU 3.0 8.1 + - - +
109B LYS 3.6 6.3 - - - +
111B TYR* 1.3 78.2 - - - +
113B ILE* 1.3 60.4 + - - +
115B HIS* 4.3 3.1 - - - -
116B PHE* 2.9 49.8 + - + +
139B GLN* 3.8 11.9 - - + +
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Residues in contact with ILE 113 (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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35B VAL* 4.3 21.1 - - + -
37B VAL* 4.7 6.1 - - + -
41B ARG* 3.3 33.4 - - - +
53B LEU* 3.8 17.9 - - + -
109B LYS* 2.9 51.7 + - + +
110B PRO* 4.1 7.6 - - + +
112B ALA* 1.3 75.7 - - - +
114B PHE* 1.3 63.8 + - - +
117B THR* 2.7 32.8 + - - +
156B GLU* 3.8 14.8 - - + +
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Residues in contact with PHE 114 (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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110B PRO 3.1 19.4 + - - +
111B TYR* 3.7 7.6 - - - +
113B ILE* 1.3 79.2 - - - +
115B HIS* 1.3 63.0 + - - +
117B THR* 3.7 2.4 + - - -
118B GLY* 3.6 11.8 + - - +
122B TYR* 3.6 38.4 - + - -
123B LEU* 3.7 16.9 - - + +
126B ILE* 4.3 13.7 - - + -
127B ARG* 6.3 0.9 - - - -
137B LEU* 3.9 30.5 - - + -
156B GLU* 3.3 21.2 + - + +
159B LEU* 4.4 13.7 - - + -
160B ILE* 3.5 31.2 - - + -
163B LEU* 4.3 11.0 - - + -
165B PHE* 6.0 1.8 - + + -
173B ARG* 3.8 4.3 - - - -
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Residues in contact with HIS 115 (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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111B TYR 3.1 19.3 + - - +
112B ALA 3.8 2.2 - - - +
113B ILE 3.3 0.2 - - - -
114B PHE* 1.3 76.1 - - - +
116B PHE* 1.3 105.4 + + - +
118B GLY 3.3 3.8 + - - -
123B LEU* 3.1 30.9 - - - +
127B ARG* 3.1 29.7 + - - +
138B ASN 4.8 0.2 - - - -
139B GLN* 3.8 31.5 + - + -
201B DGT 3.4 41.6 + + - +
10F T 4.6 1.6 - - - -
9G A 4.6 12.2 + + - -
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Residues in contact with PHE 116 (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 VAL* 3.7 21.3 - - + +
38B GLY* 2.8 27.1 + - - -
53B LEU* 4.1 17.5 - - + -
84B ARG 5.4 0.9 - - - -
102B PHE* 3.3 57.0 - + + -
103B THR 5.3 3.8 - - - -
112B ALA* 2.9 34.8 + - + +
115B HIS* 1.3 102.3 - + - +
117B THR* 1.3 61.5 + - - +
118B GLY 3.4 0.2 - - - -
139B GLN* 4.6 14.4 - - + -
201B DGT 3.3 24.4 + - - +
9G A 4.5 4.3 - - + -
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Residues in contact with THR 117 (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 VAL* 4.2 3.1 - - - +
38B GLY 4.0 6.1 - - - +
41B ARG* 2.9 42.7 + - + +
42B ARG* 2.8 32.8 + - + +
113B ILE* 2.7 24.4 + - - +
114B PHE 4.0 3.8 - - - -
116B PHE* 1.3 79.7 - - - +
118B GLY* 1.3 62.0 + - - +
170B PRO* 3.8 23.3 - - + -
173B ARG* 3.9 13.2 - - - +
201B DGT 3.5 1.3 - - - -
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Residues in contact with GLY 118 (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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42B ARG* 4.0 0.5 - - - -
114B PHE 3.6 4.8 + - - +
115B HIS 3.3 13.9 + - - -
116B PHE 3.4 0.4 - - - -
117B THR* 1.3 89.5 - - - +
119B PRO* 1.3 78.8 - - - +
122B TYR* 3.8 14.6 - - - -
123B LEU* 4.0 8.7 - - - -
173B ARG* 4.1 7.1 + - - -
201B DGT 3.6 7.4 - - - -
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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
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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