Contacts of the helix formed by residues 111 - 121 (chain B) in PDB entry 5TQB
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 PRO 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B GLU* 3.3 19.1 - - - +
110B GLY* 1.3 82.4 - - - +
112B GLU* 1.3 64.9 + - + +
113B LYS 3.2 0.7 - - - -
114B PHE* 3.0 29.0 + - + +
115B LEU* 3.4 16.2 + - + +
135B GLY* 4.0 17.5 - - - +
138B VAL* 3.8 19.0 - - + -
139B LEU* 3.5 29.8 - - + -
142B GLN* 3.8 15.5 - - - +
167B LYS* 4.4 0.2 - - - +
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Residues in contact with GLU 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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110A TRP* 4.1 11.7 - - + +
111A HIS* 3.3 16.9 - - - +
72B THR* 4.1 9.6 - - + +
76B GLN* 3.0 46.1 + - - +
91B TYR* 3.2 9.4 + - + +
109B GLY 4.6 11.6 - - - +
110B GLY 3.1 0.6 - - - -
111B PRO* 1.3 80.4 - - + +
113B LYS* 1.3 62.9 + - - +
115B LEU* 3.2 13.2 + - - +
116B TRP* 3.0 38.0 + - + +
401B PEG 3.4 18.2 - - - +
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Residues in contact with LYS 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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72B THR* 4.3 9.3 - - - +
91B TYR* 3.7 35.6 - - + +
94B ALA* 3.6 40.4 - - + -
95B VAL* 3.9 10.1 - - + +
98B ASP* 3.4 30.8 + - - -
101B GLY* 4.7 0.6 - - - -
108B GLY 3.1 22.0 + - - +
110B GLY 2.7 30.7 + - - +
112B GLU* 1.3 79.4 - - - +
114B PHE* 1.3 76.5 + - + +
116B TRP* 3.6 1.6 + - - +
117B LEU* 3.2 30.7 + - - +
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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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95B VAL* 4.1 13.2 - - + -
98B ASP 3.8 13.2 - - - -
99B GLU 3.7 13.5 - - - -
100B ASP 4.5 1.3 - - - -
101B GLY* 4.1 8.1 - - - -
111B PRO* 3.0 23.6 + - + +
113B LYS* 1.3 97.0 - - + +
115B LEU* 1.3 62.0 + - - +
117B LEU* 3.3 1.8 + - - +
118B ALA* 3.2 17.5 + - - +
131B TRP* 3.5 48.8 - + - +
134B ARG* 3.7 35.7 - - + -
135B GLY* 3.8 11.7 - - - -
138B VAL* 3.9 22.9 - - + -
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Residues in contact with LEU 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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110A TRP* 3.5 55.0 + - + +
111B PRO* 3.5 15.7 - - + +
112B GLU* 3.2 11.3 + - - +
114B PHE* 1.3 78.1 - - - +
116B TRP* 1.3 61.3 + - - +
118B ALA* 3.3 5.5 + - - +
119B GLN* 3.3 15.8 + - - +
132B PHE* 3.7 16.4 - - + +
135B GLY* 3.8 25.4 - - - -
139B LEU* 4.5 11.9 - - + -
170B ARG* 5.5 2.7 - - + -
174B THR* 3.7 32.5 - - + +
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Residues in contact with TRP 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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107A TRP* 3.7 29.2 - + - -
108A ARG 3.8 17.3 - - - -
109A LYS* 3.9 4.3 - - + -
110A TRP* 3.8 17.9 - + - +
111A HIS* 3.4 40.0 + + - -
79B VAL* 3.6 24.5 - - + -
91B TYR* 3.2 45.4 + + + -
112B GLU* 3.0 33.5 + - + +
113B LYS 4.1 2.0 - - - +
115B LEU* 1.3 75.3 - - - +
117B LEU* 1.3 59.7 + - - +
119B GLN* 3.3 19.8 + - - +
120B LEU* 2.9 58.0 + - + +
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Residues in contact with LEU 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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88B ARG* 3.8 38.8 - - + +
91B TYR* 3.9 14.4 - - + +
92B ALA* 4.0 12.1 - - + +
95B VAL* 3.4 33.0 - - + -
113B LYS 3.2 17.4 + - - +
114B PHE 3.7 4.9 - - - +
115B LEU 3.3 0.4 - - - -
116B TRP* 1.3 77.6 - - - +
118B ALA* 1.3 57.6 + - - +
120B LEU* 3.7 4.3 - - + +
121B SER* 3.0 28.9 + - - -
131B TRP* 3.7 41.3 + - + +
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Residues in contact with ALA 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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53A VAL* 5.7 0.3 - - - +
114B PHE 3.2 6.5 + - - +
115B LEU 3.4 4.3 - - - +
117B LEU* 1.3 78.6 - - - +
119B GLN* 1.3 61.2 + - - +
121B SER* 3.4 5.5 - - - -
128B SER* 2.7 52.5 + - - +
131B TRP* 3.5 15.9 - - + +
132B PHE* 3.4 32.9 - - + -
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Residues in contact with GLN 119 (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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53A VAL* 3.3 43.0 - - + +
56A LYS* 5.0 0.7 + - - -
106A ILE 3.9 4.2 - - - +
107A TRP* 4.3 13.8 - - + -
108A ARG* 3.2 44.5 + - - +
110A TRP* 3.0 25.5 + - - -
115B LEU 3.3 7.7 + - - +
116B TRP* 3.3 25.9 + - - +
118B ALA* 1.3 79.9 - - - +
120B LEU* 1.3 66.7 + - + +
121B SER 3.2 4.5 + - - +
132B PHE* 4.1 15.3 - - + -
177B ALA* 5.6 0.5 - - - +
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Residues in contact with LEU 120 (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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107A TRP* 4.2 15.0 - - + -
79B VAL* 4.5 3.8 - - + -
84B ILE* 3.8 26.0 - - + +
87B ALA* 4.1 26.2 - - + -
88B ARG* 2.9 50.5 + - + +
91B TYR* 4.5 7.9 - - + -
116B TRP* 2.9 52.0 + - + +
117B LEU* 3.7 5.6 - - - +
119B GLN* 1.3 82.0 - - + +
121B SER* 1.3 65.6 + - - +
122B GLU* 4.2 0.2 - - - -
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Residues in contact with SER 121 (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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56A LYS* 3.4 19.4 + - - -
88B ARG* 5.0 0.4 - - - +
117B LEU 3.0 12.5 + - - -
118B ALA* 3.4 17.2 - - - +
119B GLN 3.2 3.9 - - - +
120B LEU* 1.3 79.0 - - - +
122B GLU* 1.3 70.0 + - - +
123B GLU 3.4 1.6 + - - -
124B GLY* 3.0 18.7 + - - -
127B ASP* 2.6 31.7 + - - +
128B SER* 3.5 10.7 + - - -
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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