Contacts of the helix formed by residues 110 - 127 (chain A) in PDB entry 1SZU
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 THR 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A VAL* 3.6 1.4 - - - +
109A THR* 1.3 87.3 - - + +
111A GLY* 1.3 64.2 + - - +
112A SER* 3.6 6.6 + - - -
113A GLU* 3.1 26.0 + - - +
114A ALA 3.0 17.0 + - - -
277A ALA* 3.2 13.1 - - - +
1466A PLP 3.8 15.9 - - - +
109B THR* 4.0 18.4 - - + +
110B THR* 4.3 5.6 - - + -
113B GLU* 3.9 28.4 + - - +
298B TYR* 4.3 8.1 - - + +
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Residues in contact with GLY 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR* 1.3 74.5 - - - +
112A SER* 1.3 62.0 + - - +
114A ALA* 3.3 6.2 + - - +
115A VAL* 3.1 27.0 + - - +
241A ALA* 4.7 2.8 - - - +
265A THR* 5.2 0.6 - - - -
267A ALA* 3.9 20.5 - - - +
277A ALA* 3.8 3.2 - - - +
1466A PLP 3.1 34.3 + - - -
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Residues in contact with SER 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR* 3.2 5.6 - - - -
111A GLY* 1.3 76.8 - - - +
113A GLU* 1.3 58.4 + - - +
115A VAL 3.3 2.1 + - - -
116A GLU* 2.9 31.8 + - - +
139A HIS 4.0 11.0 - - - -
140A GLY* 3.3 18.9 - - - -
141A ARG* 3.4 6.2 + - - +
142A THR* 4.1 22.0 - - - -
145A THR* 3.7 8.6 - - - +
1466A PLP 2.7 23.5 + - - -
113B GLU* 5.0 6.3 + - - -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A VAL* 3.5 12.5 - - + +
109A THR* 3.0 31.5 + - - -
110A THR* 3.1 18.9 + - + +
112A SER* 1.3 76.4 - - - +
114A ALA* 1.3 60.7 + - - +
116A GLU* 3.0 10.3 + - - +
117A ASN* 2.8 42.7 + - - +
299A ALA* 5.7 0.9 - - - +
110B THR* 3.1 35.3 + - - +
112B SER* 4.4 5.9 + - - -
113B GLU* 5.5 3.8 - - + -
142B THR* 5.0 10.9 - - + +
1467B PLP 3.9 7.8 + - - -
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Residues in contact with ALA 114 (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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108A VAL* 3.7 13.6 - - + +
110A THR 3.0 13.0 + - - +
111A GLY* 3.4 11.7 - - - +
112A SER 3.2 0.4 - - - -
113A GLU* 1.3 79.0 - - - +
115A VAL* 1.3 57.2 + - - +
117A ASN* 3.2 0.4 + - - +
118A ALA* 2.9 25.6 + - - +
265A THR* 3.8 15.0 - - - -
266A PHE 4.5 1.1 - - - +
277A ALA* 4.2 2.5 - - + -
278A GLY 3.6 27.1 - - - +
279A VAL* 3.3 13.4 - - - +
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Residues in contact with VAL 115 (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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111A GLY 3.1 13.0 + - - +
112A SER 3.3 6.3 + - - +
114A ALA* 1.3 76.1 - - - +
116A GLU* 1.3 66.9 + - - +
118A ALA* 3.8 2.4 - - + +
119A VAL* 3.1 25.1 + - + +
139A HIS* 3.9 11.2 - - + +
145A THR* 3.9 8.7 - - + -
148A LEU* 3.6 30.7 - - + -
204A VAL* 4.6 10.1 - - + -
237A ILE* 5.7 1.8 - - + -
239A ASP* 3.3 35.9 - - + +
265A THR* 4.0 13.9 - - + +
1466A PLP 4.8 0.4 - - - +
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Residues in contact with GLU 116 (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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112A SER 2.9 22.0 + - - +
113A GLU* 3.0 11.0 + - - +
115A VAL* 1.3 79.2 - - - +
117A ASN* 1.3 60.1 + - - +
119A VAL* 3.7 4.3 - - - +
120A LYS* 3.0 32.2 + - - +
142A THR* 2.5 34.4 + - - +
144A TYR* 3.5 18.5 + - - +
145A THR* 4.0 5.2 - - + -
116B GLU* 4.1 0.7 - - - +
141B ARG 5.1 1.8 - - - +
142B THR* 3.5 29.3 - - + -
143B HIS* 2.8 41.4 + - - -
144B TYR 5.0 0.2 + - - -
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Residues in contact with ASN 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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106A LEU* 3.9 24.8 - - + +
108A VAL* 3.5 18.7 - - + +
113A GLU* 2.8 35.6 + - - +
114A ALA 3.8 3.1 - - - +
116A GLU* 1.3 74.5 - - - +
118A ALA* 1.3 58.6 + - - +
120A LYS* 2.9 34.8 + - - +
121A ILE* 2.8 38.6 + - + +
279A VAL* 4.3 4.5 - - + -
294A LEU* 3.7 13.6 - - + +
295A GLY 5.0 5.8 + - - +
141B ARG* 5.1 2.9 + - - +
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Residues in contact with ALA 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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114A ALA 2.9 15.9 + - - +
115A VAL* 3.3 4.7 + - - +
117A ASN* 1.3 76.4 - - - +
119A VAL* 1.3 57.3 + - - +
121A ILE* 3.5 3.2 + - - +
122A ALA* 2.9 23.0 + - - +
237A ILE* 3.8 21.3 - - + -
263A LEU* 3.4 18.0 - - + +
265A THR* 4.0 13.7 - - + -
279A VAL* 4.0 24.1 - - + +
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Residues in contact with VAL 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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115A VAL* 3.1 25.4 + - + +
116A GLU* 3.7 3.6 - - - +
118A ALA* 1.3 74.3 - - - +
120A LYS* 1.3 59.0 + - - +
122A ALA* 3.0 3.6 + - + +
123A ARG* 2.8 41.5 + - + +
131A THR* 3.7 24.5 - - + -
144A TYR* 3.9 17.9 - - + +
148A LEU* 4.4 0.4 - - + -
202A ALA* 5.7 0.2 - - - -
204A VAL* 4.2 17.3 - - + -
237A ILE* 4.1 17.5 - - + -
143B HIS* 3.6 23.8 - - + +
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Residues in contact with LYS 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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116A GLU 3.0 17.5 + - - +
117A ASN* 2.9 39.9 + - - +
119A VAL* 1.3 75.1 - - - +
121A ILE* 1.3 63.9 + - + +
123A ARG* 3.3 7.0 + - - +
124A ALA* 3.0 19.6 + - - +
289A VAL* 4.7 1.3 - - - -
293A GLY 4.1 14.9 + - - -
294A LEU* 4.5 6.2 - - + +
295A GLY 5.6 0.2 + - - -
141B ARG* 2.8 38.5 + - - +
142B THR* 5.4 0.2 - - - -
143B HIS* 3.7 19.3 - - + +
146B LEU* 3.8 25.2 - - + +
155B TYR 4.9 0.2 + - - -
159B MET* 3.5 34.8 - - + +
162B MET* 5.6 0.4 - - + -
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Residues in contact with ILE 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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106A LEU* 4.6 2.5 - - + -
117A ASN* 2.8 30.0 + - + +
118A ALA* 3.6 7.0 - - - +
120A LYS* 1.3 73.0 - - - +
122A ALA* 1.3 66.1 + - - +
124A ALA* 3.1 2.9 + - - +
125A ALA* 2.9 22.5 + - - +
263A LEU* 4.1 8.3 - - + -
279A VAL* 4.5 4.0 - - + -
285A VAL* 3.3 38.2 - - + +
286A MET* 3.9 33.7 - - + +
289A VAL* 3.8 22.7 - - + -
294A LEU* 4.3 22.2 - - + -
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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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118A ALA 2.9 19.5 + - - +
119A VAL* 3.0 5.4 + - - +
121A ILE* 1.3 76.0 - - - +
123A ARG* 1.3 60.7 + - - +
125A ALA* 3.3 2.0 + - - +
126A THR* 2.9 32.7 + - - +
201A ALA* 4.0 4.5 - - + +
202A ALA* 3.8 28.3 - - + -
235A MET* 3.9 22.0 - - + -
237A ILE* 4.1 1.3 - - + -
263A LEU* 4.0 7.0 - - + -
285A VAL* 5.0 0.2 - - - -
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Residues in contact with ARG 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 VAL* 2.8 32.9 + - + +
120A LYS* 3.6 6.7 - - - +
122A ALA* 1.3 73.6 - - - +
124A ALA* 1.3 57.7 + - - +
127A LYS* 2.8 31.2 + - - -
128A ARG 3.3 18.0 + - - +
129A SER* 3.4 38.7 + - - +
131A THR* 5.4 0.2 - - + -
144A TYR* 4.7 7.7 - - - -
201A ALA* 3.8 11.7 - - + -
143B HIS* 3.0 40.6 + - - -
158B GLY 3.4 4.5 - - - +
159B MET* 2.9 34.5 + - - +
160B GLY 3.9 3.4 - - - -
161B LEU 3.0 26.1 + - - -
162B MET* 4.0 6.5 - - - +
163B PRO* 5.6 0.6 - - - +
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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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120A LYS 3.0 16.6 + - - +
121A ILE 3.1 4.2 + - - +
123A ARG* 1.3 76.9 - - - +
125A ALA* 1.3 61.5 + - - +
127A LYS* 3.9 16.5 + - - +
288A ALA* 3.8 18.6 - - + +
289A VAL* 3.7 24.0 - - + -
157B ALA 4.3 7.0 - - - +
158B GLY* 3.7 16.5 - - - +
159B MET* 4.1 10.0 - - + +
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Residues in contact with ALA 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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121A ILE 2.9 15.8 + - - +
122A ALA* 3.8 4.3 - - - +
124A ALA* 1.3 79.8 - - - +
126A THR* 1.3 63.9 + - + +
127A LYS* 5.0 2.1 - - - +
235A MET* 5.0 1.3 - - - -
284A GLU 5.2 0.2 - - - +
285A VAL* 4.0 29.4 - - + +
288A ALA* 3.4 20.4 - - + -
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Residues in contact with THR 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 2.9 20.9 + - - +
123A ARG 3.7 0.2 + - - -
125A ALA* 1.3 79.3 - - - +
127A LYS* 1.3 73.7 + - - +
128A ARG* 3.3 29.3 + - - +
201A ALA* 3.3 25.4 - - - +
233A GLY 3.7 21.1 - - - +
235A MET* 3.8 25.6 - - + -
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Residues in contact with LYS 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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123A ARG 2.8 12.7 + - - -
124A ALA 4.3 10.7 + - - +
125A ALA 3.6 2.6 - - - +
126A THR* 1.3 81.6 - - - +
128A ARG* 1.3 61.3 + - - +
158B GLY* 4.1 28.6 - - - +
159B MET 5.8 0.7 - - - -
198D GLU* 5.4 3.0 + - - -
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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