Contacts of the helix formed by residues 111 - 130 (chain A) 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 HIS 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LYS* 4.1 16.0 - - + +
110A TRP* 1.3 72.0 - - - +
112A VAL* 1.3 63.5 + - - +
113A LYS 3.4 2.0 - - - -
114A ILE* 3.3 26.9 + - + -
115A ASN* 3.4 9.0 + - + +
76B GLN* 3.9 20.3 - - + +
79B VAL* 4.1 13.5 - - + -
80B GLU* 2.7 32.0 + - + +
112B GLU* 3.3 18.8 + - - +
116B TRP* 3.4 37.5 + + - -
401B PEG 3.7 23.6 - - - +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LYS 4.1 4.7 - - - +
110A TRP 2.8 18.7 + - - +
111A HIS* 1.3 70.8 - - - +
113A LYS* 1.3 62.8 + - + +
115A ASN* 3.0 10.7 + - + +
116A GLN* 2.8 56.0 + - + +
170B ARG* 3.8 24.9 - - - +
401B PEG 3.4 12.9 + - - +
405B EDO 3.7 29.4 - - - -
407B EDO 4.3 11.4 - - - +
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A HIS 3.4 0.6 - - - -
112A VAL* 1.3 81.2 - - - +
114A ILE* 1.3 59.0 + - + +
116A GLN* 3.3 32.9 + - - +
117A GLY* 2.9 25.6 + - - -
120A ARG* 5.5 0.5 + - - -
42B GLU* 4.0 11.4 - - - +
166B ASP* 3.7 31.5 + - - -
170B ARG* 5.1 1.0 - - - +
401B PEG 3.5 35.7 + - - +
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A HIS* 3.5 23.8 - - + +
112A VAL 3.2 0.4 - - - -
113A LYS* 1.3 78.3 - - + +
115A ASN* 1.3 58.1 + - - +
117A GLY* 3.1 3.1 + - - -
118A GLN* 2.9 44.2 + - - +
38B THR* 4.1 17.9 - - + -
41B LEU* 3.8 35.4 - - + +
42B GLU* 4.0 22.5 - - + +
73B LEU* 5.6 0.4 - - + -
76B GLN* 3.8 20.0 - - - +
80B GLU* 4.6 1.8 - - - +
401B PEG 3.6 18.8 - - - +
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Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A HIS 5.1 0.2 - - - +
39A VAL* 3.1 28.0 - - - +
109A LYS* 4.1 16.3 + - + +
111A HIS* 3.4 11.2 + - + +
112A VAL* 3.0 12.7 + - + +
114A ILE* 1.3 79.8 - - - +
116A GLN* 1.3 65.5 + - - +
118A GLN* 3.3 15.0 + - - +
119A LYS* 3.1 44.2 + - - +
302A EDO 3.2 19.8 + - - -
80B GLU* 5.9 0.9 - - - +
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 2.8 42.0 + - + +
113A LYS* 3.6 32.1 + - - +
115A ASN* 1.3 82.8 - - - +
117A GLY* 1.3 61.8 + - - +
119A LYS* 3.3 13.8 + - + +
120A ARG* 3.2 35.5 + - - +
166B ASP* 5.8 0.4 + - - -
249B PRO* 4.5 24.1 + - + +
407B EDO 5.6 3.8 - - - -
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS 2.9 15.3 + - - -
114A ILE 3.1 3.8 + - - -
116A GLN* 1.3 75.7 - - - +
118A GLN* 1.3 58.4 + - - +
120A ARG* 3.2 26.4 + - - +
121A PHE* 3.0 23.7 + - - +
42B GLU* 3.5 23.7 - - - +
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 4.2 9.5 - - + +
38A HIS* 3.6 23.2 + - - -
39A VAL* 3.9 14.9 - - + +
114A ILE* 2.9 22.0 + - - +
115A ASN* 3.6 21.9 - - - +
116A GLN 3.2 0.2 - - - -
117A GLY* 1.3 74.3 - - - +
119A LYS* 1.3 60.8 + - - +
121A PHE* 3.9 1.8 - - - +
122A ALA* 2.9 30.1 + - - +
41B LEU* 3.1 23.8 + - - +
42B GLU* 3.4 17.9 - - - +
44B GLY* 4.5 9.1 - - - +
46B ILE* 5.1 0.8 - - - +
80B GLU* 3.0 29.5 + - - +
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 3.4 35.9 - - + -
40A HIS* 4.8 5.4 - - - -
115A ASN* 3.1 25.8 + - - +
116A GLN* 3.5 16.1 - - + +
118A GLN* 1.3 76.9 - - - +
120A ARG* 1.3 62.2 + - - +
122A ALA* 3.4 7.8 + - - +
123A THR* 3.2 25.3 + - - -
242A LEU* 4.1 16.0 - - + +
302A EDO 3.4 22.8 + - - -
246B PRO 5.9 0.8 + - - -
247B GLU* 5.3 18.0 + - + +
248B ASP 5.7 2.6 + - - -
249B PRO* 6.3 0.6 - - - +
251B VAL* 5.2 7.5 + - - +
407B EDO 5.6 5.7 - - - -
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS 5.5 0.6 + - - -
116A GLN* 3.2 27.0 + - - +
117A GLY* 3.2 31.3 + - - +
119A LYS* 1.3 80.2 - - - +
121A PHE* 1.3 61.8 + - - +
123A THR* 3.3 18.1 + - - -
269A TYR* 2.9 34.9 + - + +
272A LYS 4.1 21.1 + - - +
42B GLU* 4.8 6.9 + - - -
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Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 4.8 5.8 - - + -
30A PRO* 3.3 42.6 - - + -
32A ARG* 3.4 28.7 - - + -
35A ILE* 4.1 15.9 - - + -
117A GLY 3.0 7.3 + - - +
118A GLN 3.9 1.3 - - - +
120A ARG* 1.3 74.0 - - - +
122A ALA* 1.3 63.4 + - - +
124A ALA* 2.8 11.3 + - + +
125A SER* 2.8 38.9 + - - -
269A TYR* 4.0 6.3 - - - -
42B GLU 3.7 18.4 - - - +
43B GLU* 3.2 42.4 - - + -
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ILE* 3.8 33.2 - - + +
36A VAL* 4.1 8.1 - - + +
39A VAL* 4.8 3.8 - - + -
118A GLN 2.9 19.1 + - - +
119A LYS* 3.5 9.4 - - - +
121A PHE* 1.3 76.6 - - - +
123A THR* 1.3 57.7 + - - +
125A SER* 3.2 3.0 + - - -
126A ALA* 2.8 31.9 + - - +
242A LEU* 3.8 15.6 - - + +
251A LEU* 4.8 0.9 - - - +
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LYS 3.2 12.0 + - - -
120A ARG* 3.4 12.3 - - - -
121A PHE 3.1 0.4 - - - -
122A ALA* 1.3 79.4 - - - +
124A ALA* 1.3 60.5 + - - +
126A ALA* 3.5 3.1 + - - +
127A LEU* 3.2 28.9 + - + +
240A LEU* 5.0 11.6 + - + +
241A ASN* 5.5 0.9 - - - -
242A LEU* 3.6 22.2 + - - +
245A LEU* 4.2 17.2 - - + +
269A TYR* 4.2 17.5 - - + -
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.7 25.2 - - + +
29A ALA* 4.1 13.2 - - + -
120A ARG 3.5 1.8 + - - -
121A PHE* 2.8 12.8 + - + +
123A THR* 1.3 79.3 - - - +
125A SER* 1.3 60.0 - - - +
127A LEU* 3.2 4.2 + - - +
128A ALA* 3.0 26.7 + - - +
269A TYR* 3.3 30.9 + - + +
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA* 4.5 2.9 - - - +
30A PRO 2.9 26.9 + - - -
31A ILE* 3.4 3.1 - - - +
32A ARG* 3.2 19.2 + - - -
35A ILE* 4.4 2.5 - - - -
121A PHE* 2.8 26.9 + - - -
122A ALA* 3.6 7.6 - - - -
124A ALA* 1.3 76.9 - - - +
126A ALA* 1.3 58.3 + - - +
128A ALA* 3.4 5.9 + - - +
129A ALA* 3.0 27.0 + - - +
251A LEU* 3.8 11.1 - - - +
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ALA 2.8 17.3 + - - +
123A THR 3.9 4.0 - - - +
125A SER* 1.3 76.1 - - - +
127A LEU* 1.3 65.5 + - - +
129A ALA* 3.4 5.4 + - - +
130A SER* 3.2 21.3 + - - -
242A LEU* 4.5 4.0 - - + -
245A LEU* 3.8 38.4 - - + +
246A ALA* 4.5 2.2 - - + -
251A LEU* 3.7 24.2 - - + +
252A GLY 4.8 0.7 + - - -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.9 33.9 - - + -
27A PHE* 3.2 13.7 - - + -
123A THR* 3.2 30.7 + - + +
124A ALA* 3.5 8.1 - - - +
126A ALA* 1.3 78.8 - - - +
128A ALA* 1.3 60.8 + - - +
130A SER* 2.5 25.5 + - - -
240A LEU* 4.3 14.4 - - + -
245A LEU* 4.4 16.6 - - + -
255A ILE* 4.7 4.5 - - + -
257A TRP* 3.8 35.2 - - + -
265A LEU* 4.5 12.6 - - + -
269A TYR* 5.0 7.0 - - + -
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL 4.1 2.0 + - - +
27A PHE* 3.6 30.6 - - - +
29A ALA 3.5 24.9 - - - +
31A ILE* 3.9 10.3 - - + +
124A ALA 3.0 12.3 + - - +
125A SER 3.7 8.5 - - - +
126A ALA 3.3 0.2 - - - -
127A LEU* 1.3 78.2 - - - +
129A ALA* 1.3 62.0 + - - +
131A ALA* 3.0 16.8 + - - +
132A VAL* 3.6 11.6 - - - +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 3.8 13.9 - - + +
125A SER 3.0 16.8 + - - +
126A ALA 3.6 5.4 - - - +
127A LEU 3.3 0.4 - - - -
128A ALA* 1.3 76.6 - - - +
130A SER* 1.3 61.7 + - - +
131A ALA 3.1 1.2 + - - -
132A VAL* 3.1 20.8 + - - +
135A LEU* 3.7 20.7 - - + +
136A LEU* 4.2 0.5 - - - +
251A LEU* 3.6 31.0 - - + -
252A GLY* 3.9 8.4 - - - +
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.7 9.9 - - - -
126A ALA 3.2 11.7 + - - -
127A LEU* 2.5 21.4 + - - -
128A ALA 3.1 0.2 - - - -
129A ALA* 1.3 77.6 - - - +
131A ALA* 1.3 55.6 + - - +
132A VAL 3.3 0.9 - - - -
136A LEU* 3.4 12.6 - - - +
252A GLY* 4.5 0.4 - - - -
253A ARG* 3.2 27.1 - - - +
255A ILE* 3.7 23.9 - - - +
257A TRP* 4.8 3.3 + - - -
301A EDO 2.8 30.5 + - - -
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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
------------------------------------------------------------
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