Contacts of the helix formed by residues 110 - 127 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A THR* 3.7 31.9 - - + +
110A THR* 4.3 4.0 - - + -
113A GLU* 3.1 25.9 + - - +
298A TYR* 4.2 7.4 - - + +
108B VAL* 3.6 0.3 - - - +
109B THR* 1.3 83.0 - - + +
111B GLY* 1.3 64.7 + - - +
112B SER* 3.9 0.3 - - - -
113B GLU* 3.1 27.1 + - - +
114B ALA 3.1 17.7 + - - -
277B ALA* 3.2 12.2 - - - +
1467B PLP 3.6 18.7 + - - +
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B THR* 1.3 70.8 - - - +
112B SER* 1.3 61.5 + - - +
114B ALA* 3.2 6.2 + - - +
115B VAL* 3.1 26.7 + - - +
241B ALA* 4.9 2.2 - - - +
265B THR* 5.2 0.6 + - - -
267B ALA* 4.0 20.8 - - - +
277B ALA* 3.7 4.4 - - - +
1467B PLP 2.9 37.2 + - - -
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU* 4.4 4.6 + - - -
110B THR* 3.9 4.5 - - - -
111B GLY* 1.3 73.9 - - - +
113B GLU* 1.3 60.4 + - - +
115B VAL 3.3 1.2 + - - -
116B GLU* 2.9 33.8 + - - +
139B HIS 3.9 9.9 - - - -
140B GLY* 3.2 21.7 - - - -
141B ARG 3.3 6.1 + - - -
142B THR* 4.0 22.7 - - - -
145B THR* 3.6 8.2 - - - +
1467B PLP 2.7 23.7 + - - -
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A THR* 3.9 25.3 + - - +
112A SER* 5.0 3.6 + - - -
113A GLU* 5.5 3.6 - - + +
142A THR* 5.1 13.0 - - + -
1466A PLP 4.5 6.9 + - - -
108B VAL* 3.8 14.2 - - + +
109B THR* 2.7 38.1 + - - -
110B THR* 3.1 22.0 + - - +
112B SER* 1.3 74.4 - - - +
114B ALA* 1.3 61.8 + - - +
116B GLU* 3.1 8.3 + - - +
117B ASN* 2.8 41.9 + - - +
142B THR* 5.5 0.9 - - + +
295B GLY 5.0 6.2 - - - +
296B GLY* 5.2 5.2 - - - -
299B ALA* 5.9 1.2 + - - +
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Residues in contact with ALA 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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108B VAL* 3.8 5.6 - - + +
110B THR 3.1 12.0 + - - +
111B GLY* 3.4 13.0 - - - +
113B GLU* 1.3 76.9 - - - +
115B VAL* 1.3 57.9 + - - +
117B ASN* 3.2 1.4 + - - -
118B ALA* 2.8 27.0 + - - +
265B THR* 3.6 13.7 - - - -
266B PHE 4.5 1.3 - - - +
277B ALA* 4.3 0.9 - - + -
278B GLY 3.4 34.3 - - - +
279B VAL* 3.3 14.4 - - - +
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Residues in contact with VAL 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 GLY 3.1 13.4 + - - +
112B SER 3.3 5.8 + - - +
114B ALA* 1.3 75.0 - - - +
116B GLU* 1.3 65.5 + - - +
118B ALA* 3.3 2.4 + - + +
119B VAL* 3.1 27.3 + - + +
139B HIS* 3.7 14.6 - - + +
145B THR* 3.7 9.4 - - + -
148B LEU* 3.5 31.9 - - + -
204B VAL* 4.6 11.0 - - + -
237B ILE* 6.2 0.2 - - + -
239B ASP* 3.3 34.1 - - + +
265B THR* 4.0 14.1 - - + +
1467B PLP 4.7 0.7 - - - +
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Residues in contact with GLU 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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116A GLU* 4.1 0.5 - - - +
141A ARG 5.2 1.6 - - - +
142A THR* 3.5 28.5 - - + -
143A HIS* 2.7 42.7 + - - -
144A TYR 5.1 0.2 + - - -
112B SER 2.9 24.4 + - - +
113B GLU* 3.3 10.5 - - - +
115B VAL* 1.3 79.5 - - - +
117B ASN* 1.3 60.2 + - - +
119B VAL* 3.4 4.5 + - - +
120B LYS* 3.0 32.0 + - - +
142B THR* 2.4 34.0 + - - +
144B TYR* 3.5 18.7 + - - +
145B THR* 3.9 6.1 - - + -
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Residues in contact with ASN 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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141A ARG* 5.3 3.3 + - - +
106B LEU* 3.7 23.9 - - + +
108B VAL* 3.4 20.8 - - - +
113B GLU* 2.8 35.2 + - - +
114B ALA 3.9 2.7 - - - +
116B GLU* 1.3 73.7 - - - +
118B ALA* 1.3 67.4 + - - +
120B LYS* 2.9 35.3 + - - +
121B ILE* 2.9 32.1 + - + +
279B VAL* 4.3 4.0 - - + -
294B LEU* 3.8 12.3 - - - +
295B GLY 5.2 6.9 + - - +
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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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114B ALA 2.8 21.0 + - - +
115B VAL 3.6 4.9 - - - +
117B ASN* 1.3 73.9 - - - +
119B VAL* 1.3 57.4 + - - +
121B ILE* 3.4 4.3 + - - +
122B ALA* 3.0 23.9 + - - +
237B ILE* 3.8 24.0 - - + -
263B LEU* 3.6 13.3 - - + +
265B THR* 3.8 19.3 - - + -
279B VAL* 4.0 19.0 - - + +
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Residues in contact with VAL 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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143A HIS* 3.6 23.6 - - + +
115B VAL* 3.1 19.1 + - + +
116B GLU 3.7 4.0 - - - +
118B ALA* 1.3 73.9 - - - +
120B LYS* 1.3 65.0 + - - +
122B ALA* 3.2 3.6 + - + +
123B ARG* 2.9 29.0 + - + +
131B THR* 3.7 26.5 - - + -
144B TYR* 3.7 19.5 - - + +
148B LEU* 4.3 11.9 - - + -
204B VAL* 4.4 10.3 - - + -
237B ILE* 4.1 17.7 - - + -
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Residues in contact with LYS 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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141A ARG* 3.0 38.1 + - - +
143A HIS* 3.8 19.3 - - + +
146A LEU* 3.6 27.1 - - + +
155A TYR 4.8 0.4 + - - -
159A MET* 3.6 25.6 - - + +
162A MET* 5.5 0.9 - - + -
116B GLU 3.0 17.3 + - - +
117B ASN* 2.9 38.2 + - - +
119B VAL* 1.3 75.2 - - - +
121B ILE* 1.3 64.7 + - + +
123B ARG* 3.2 10.6 + - - +
124B ALA* 3.0 24.5 + - - +
289B VAL* 4.8 1.1 - - + -
293B GLY 3.9 16.4 + - - -
294B LEU* 4.6 5.8 - - + +
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Residues in contact with ILE 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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106B LEU* 4.4 9.2 - - + -
117B ASN 2.9 25.2 + - - +
118B ALA* 3.6 4.3 - - - +
120B LYS* 1.3 77.2 - - - +
122B ALA* 1.3 61.7 + - - +
124B ALA* 3.2 2.3 + - - +
125B ALA* 2.9 22.5 + - - +
263B LEU* 4.1 8.7 - - + -
279B VAL* 4.4 6.1 - - + -
285B VAL* 3.3 35.5 - - + +
286B MET* 3.8 38.1 - - + +
289B VAL* 4.0 22.2 - - + -
294B LEU* 4.2 19.7 - - + -
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Residues in contact with ALA 122 (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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118B ALA 3.0 17.1 + - - +
119B VAL* 3.2 4.9 + - + +
121B ILE* 1.3 76.0 - - - +
123B ARG* 1.3 57.6 + - - +
125B ALA* 3.4 2.5 + - - +
126B THR* 2.9 36.5 + - - +
201B ALA* 3.8 13.2 - - + +
202B ALA* 3.8 16.6 - - + -
235B MET* 3.8 27.8 - - + -
237B ILE* 4.3 1.1 - - + -
263B LEU* 4.2 6.3 - - + +
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Residues in contact with ARG 123 (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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143A HIS* 3.1 37.8 + - - -
158A GLY 4.1 4.1 - - - +
159A MET* 2.9 33.8 + - - +
160A GLY 3.9 0.8 - - - -
161A LEU 2.9 31.1 + - - -
162A MET* 4.0 5.9 - - - +
163A PRO* 5.7 1.0 - - - +
119B VAL* 2.9 29.6 + - + +
120B LYS* 3.5 6.7 - - - +
121B ILE 3.2 0.2 - - - -
122B ALA* 1.3 77.2 - - - +
124B ALA* 1.3 54.5 + - - +
127B LYS* 2.7 35.3 + - - -
128B ARG 3.2 19.8 + - - +
129B SER* 3.5 37.0 + - - +
144B TYR* 4.5 8.5 - - - -
201B ALA* 3.8 11.9 - - + -
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Residues in contact with ALA 124 (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 ALA 5.1 0.9 - - - +
158A GLY* 3.6 21.0 - - - +
159A MET* 4.2 8.5 - - + +
120B LYS 3.0 16.1 + - - +
121B ILE 3.2 3.6 + - - +
123B ARG* 1.3 78.1 - - - +
125B ALA* 1.3 63.6 + - - +
126B THR 3.6 0.2 + - - -
127B LYS* 3.7 18.4 + - - +
288B ALA* 3.8 18.3 - - + +
289B VAL* 3.8 22.9 - - + -
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Residues in contact with ALA 125 (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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121B ILE 2.9 17.1 + - - +
122B ALA* 3.8 4.3 - - - +
124B ALA* 1.3 79.7 - - - +
126B THR* 1.3 63.1 + - + +
127B LYS* 5.1 1.7 - - - +
235B MET* 5.0 1.6 - - + -
285B VAL* 3.7 32.5 - - + -
288B ALA* 3.4 18.1 - - + +
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Residues in contact with THR 126 (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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122B ALA 2.9 24.2 + - - +
125B ALA* 1.3 78.9 - - - +
127B LYS* 1.3 71.1 + - - +
128B ARG* 3.3 42.3 + - - +
201B ALA* 3.4 13.1 - - - +
233B GLY 3.5 23.6 - - - +
235B MET* 3.8 25.4 - - + -
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Residues in contact with LYS 127 (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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158A GLY* 4.8 13.0 + - - +
159A MET 6.4 0.4 - - - -
123B ARG 2.7 16.2 + - - -
124B ALA 4.0 13.6 + - - +
125B ALA 3.4 1.5 - - - +
126B THR* 1.3 82.0 - - - +
128B ARG* 1.3 58.3 + - - +
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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