Contacts of the helix formed by residues 127 - 144 (chain B) in PDB entry 1T0R
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 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ALA 3.3 15.9 - - - +
123B ARG 3.2 24.5 - - - +
125B TYR 3.5 2.2 - - - -
126B THR* 1.3 97.7 - - - +
128B ALA* 1.3 56.2 + - - -
129B ARG 2.9 7.2 + - - -
130B TYR* 3.0 21.9 + - - +
131B LEU 4.0 0.9 + - - -
189B GLU* 3.6 35.4 - - + +
192B VAL* 4.0 7.4 - - + -
193B TRP* 4.5 9.7 - - + +
199B TRP* 3.6 23.1 - - + +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B TYR* 2.9 20.5 + - + +
126B THR 2.9 1.0 + - - -
127B PRO* 1.3 79.8 - - - +
129B ARG* 1.3 56.3 + - - +
130B TYR 3.0 0.2 - - - -
131B LEU* 3.1 4.0 + - - +
132B PHE* 2.8 49.3 + - + -
169B THR* 4.8 3.1 - - + -
199B TRP* 4.0 10.8 - - + -
234B LEU* 3.4 30.1 - - + -
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.6 37.6 + - - +
15A THR* 2.9 33.9 + - - +
16A THR* 4.3 3.5 - - + +
126B THR 3.1 12.2 + - - +
127B PRO 2.9 1.8 + - - -
128B ALA* 1.3 78.7 - - - +
130B TYR* 1.3 97.7 + - + +
132B PHE* 4.5 5.4 - - - -
133B HIS* 3.2 24.6 + - - +
166B LEU* 4.1 19.6 - - + +
169B THR* 4.0 16.9 - - + +
170B ALA* 5.3 4.9 - - - +
173B THR* 4.7 5.8 + - - +
186B GLY* 3.7 15.0 + - - -
187B LYS 5.6 0.6 + - - -
189B GLU* 3.2 34.4 + - - +
190B ARG* 4.7 1.8 - - - +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR* 3.2 28.6 + - - +
16A THR* 3.4 18.8 - - - -
17A ASN 3.4 22.9 + - - -
18A TRP* 4.3 10.1 - + + -
127B PRO 3.0 14.8 + - - +
128B ALA 3.0 0.2 - - - -
129B ARG* 1.3 110.9 + - + +
131B LEU* 1.3 60.4 + - - +
133B HIS* 3.5 3.8 + - - +
134B ALA* 3.0 28.2 + - - +
189B GLU* 3.8 4.7 - - + -
190B ARG* 3.5 39.2 - - + +
193B TRP* 3.6 46.0 - + + +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PRO 4.0 1.0 + - - -
128B ALA* 3.1 10.3 + - - +
130B TYR* 1.3 79.3 - - - +
132B PHE* 1.3 59.5 + - + +
134B ALA* 3.4 4.4 + - - +
135B LEU* 3.0 28.8 + - + +
193B TRP* 4.0 15.8 - - + -
199B TRP* 3.9 23.6 - - + -
202B PHE* 3.9 20.6 - - + +
206B ILE* 3.5 39.5 - - + -
230B VAL* 3.8 41.3 - - + -
234B LEU* 4.1 6.3 - - + -
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Residues in contact with PHE 132 (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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125B TYR* 5.9 3.8 - + - -
128B ALA* 2.8 33.2 + - + +
129B ARG 4.1 1.3 - - - +
131B LEU* 1.3 77.7 - - + +
133B HIS* 1.3 63.6 + - - +
135B LEU* 3.4 13.3 + - + +
136B GLN* 3.1 19.2 + - - +
162B HIS* 4.1 9.5 - - - +
165B TRP* 3.7 43.3 - + + -
166B LEU* 4.1 17.7 - - - +
169B THR* 3.5 26.2 - - - -
230B VAL* 4.1 14.1 - - + -
234B LEU* 4.1 20.4 - - + -
235B LEU* 4.2 22.9 - - + -
257B GLN* 4.5 7.4 - - - -
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Residues in contact with HIS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 3.2 39.6 + - + +
18A TRP* 5.0 1.1 - + - -
115A ALA 5.2 1.1 - - - -
121A PRO 5.2 0.4 - - - -
124A ARG* 2.7 42.8 + - + -
125A ASN* 3.4 22.0 + - - -
129B ARG 3.2 19.2 + - - +
130B TYR 4.0 2.9 - - - +
132B PHE* 1.3 73.4 - - - +
134B ALA* 1.3 61.6 + - - +
136B GLN* 2.8 47.7 + - - +
137B MET* 2.8 32.0 + - + +
166B LEU* 3.8 8.4 - - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 4.2 11.9 - - + -
130B TYR 3.0 17.5 + - - +
131B LEU* 3.4 4.9 - - + +
133B HIS* 1.3 77.7 - - - +
135B LEU* 1.3 55.4 + - - +
137B MET* 3.2 16.1 + - - +
138B GLY* 2.9 24.9 + - - -
206B ILE* 3.2 38.1 - - + -
210B LEU* 3.8 10.3 - - + +
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Residues in contact with LEU 135 (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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131B LEU* 3.0 23.2 + - + +
132B PHE* 3.6 18.4 - - + +
134B ALA* 1.3 72.1 - - - +
136B GLN* 1.3 56.4 + - - +
138B GLY* 3.1 3.4 + - - +
139B SER* 2.7 31.0 + - - -
162B HIS* 3.1 33.0 + - + +
165B TRP* 4.5 7.4 - - + -
206B ILE* 5.0 3.8 - - + -
222B ILE* 4.8 11.5 - - + +
226B THR* 4.1 22.2 - - + -
227B LYS* 3.6 28.7 - - + -
230B VAL* 4.1 27.6 - - + -
231B GLU* 6.4 0.2 - - + -
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Residues in contact with GLN 136 (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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115A ALA 5.8 2.3 + - - +
124A ARG 4.5 0.6 + - - -
125A ASN* 3.3 18.0 + - - +
128A THR* 3.0 26.4 + - - +
132B PHE 3.1 9.4 + - - +
133B HIS* 2.8 37.6 + - + +
135B LEU* 1.3 77.9 - - - +
137B MET* 1.3 60.3 + - - +
139B SER* 3.1 3.4 + - - -
140B VAL* 2.9 26.0 + - + +
159B THR* 3.8 22.6 - - + +
162B HIS* 3.6 13.5 - - + -
163B LEU* 3.5 24.6 + - - +
166B LEU* 3.5 17.2 - - - +
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Residues in contact with MET 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 4.2 22.0 - - + -
28A LEU* 5.4 1.8 - - + -
29A PHE* 4.1 18.2 - - + -
115A ALA 4.2 11.0 - - - +
116A ARG* 3.3 53.4 - - - +
124A ARG* 4.1 7.4 - - - +
133B HIS* 2.8 48.6 + - + +
134B ALA* 3.4 9.4 - - - +
136B GLN* 1.3 76.1 - - - +
138B GLY* 1.3 62.7 + - - +
140B VAL* 3.3 11.8 - - - +
141B TYR* 3.1 18.0 + - - +
210B LEU* 4.4 10.5 - - + -
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Residues in contact with GLY 138 (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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134B ALA 2.9 12.1 + - - -
135B LEU* 3.1 4.2 + - - -
137B MET* 1.3 79.3 - - - +
139B SER* 1.3 60.0 + - - +
141B TYR* 3.4 12.3 + - - +
142B ILE* 3.4 17.7 + - - +
210B LEU* 3.6 19.7 - - - +
218B ALA* 5.7 0.2 - - - +
222B ILE* 4.2 22.9 - - - +
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Residues in contact with SER 139 (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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135B LEU 2.7 9.5 + - - -
136B GLN 3.1 5.7 + - - -
138B GLY* 1.3 70.0 - - - +
140B VAL* 1.3 63.4 + - - +
141B TYR 3.1 0.7 - - - -
142B ILE* 3.5 10.2 + - - +
143B HIS 3.3 15.1 + - - -
155B ALA* 3.7 12.8 - - - +
158B GLU* 3.5 24.0 - - - -
159B THR* 2.8 26.9 + - - -
162B HIS* 2.8 34.7 - - - -
222B ILE* 4.7 3.0 - - - +
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Residues in contact with VAL 140 (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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112A ALA* 3.8 10.1 - - + +
115A ALA* 3.7 23.1 - - + +
116A ARG* 3.3 40.2 - - + +
131A MET* 3.6 31.4 - - + -
136B GLN* 2.9 16.1 + - + +
137B MET* 3.3 11.4 - - - +
138B GLY 3.3 0.2 - - - -
139B SER* 1.3 75.5 - - - +
141B TYR* 1.3 64.0 + - - +
143B HIS* 3.5 13.0 - - + +
144B GLN* 3.2 14.4 + - - +
159B THR* 3.2 15.0 + - + +
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Residues in contact with TYR 141 (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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33A MET* 4.9 0.4 - - + -
116A ARG* 4.0 10.1 - - + +
117A PHE* 3.8 25.8 - + - -
57B TRP* 2.9 32.2 + - - -
137B MET 3.1 16.6 + - - +
138B GLY* 3.7 6.5 - - - +
139B SER 3.1 0.6 - - - -
140B VAL* 1.3 77.9 - - - +
142B ILE* 1.3 67.9 + - - +
144B GLN* 3.1 33.1 + - + +
145B ILE* 3.3 28.4 + - + +
210B LEU* 5.6 2.0 - - + +
212B ALA 4.0 4.0 - - - -
213B TRP* 2.8 60.1 + + - -
218B ALA* 4.4 14.4 - - + -
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Residues in contact with ILE 142 (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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138B GLY 3.4 15.3 + - - +
139B SER* 3.7 11.2 - - - +
140B VAL 3.4 0.2 - - - -
141B TYR* 1.3 76.8 - - - +
143B HIS* 1.3 58.8 + - - +
145B ILE* 4.4 7.6 - - + -
146B ALA* 2.9 38.6 + - + +
151B ILE* 5.2 4.0 - - + -
155B ALA* 4.1 12.8 - - + -
158B GLU* 5.2 0.4 - - - +
215B TRP* 5.3 6.7 - - + +
218B ALA* 3.9 37.0 - - + +
219B PHE* 3.9 18.4 - - + +
222B ILE* 4.1 17.3 - - + -
223B ASN* 4.1 11.2 - - - +
267B TRP* 4.8 12.3 - - + -
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Residues in contact with HIS 143 (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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105A TYR* 5.3 1.1 - + - -
108A SER* 2.9 30.4 + - - -
109A THR* 3.6 18.7 + - - -
112A ALA* 3.6 16.6 - - + -
131A MET* 3.9 11.1 - - - -
36B HIS* 4.6 1.9 + - - -
139B SER 3.3 6.4 + - - +
140B VAL* 3.5 13.5 - - + +
141B TYR 3.1 0.4 - - - -
142B ILE* 1.3 81.1 - - - +
144B GLN* 1.3 63.6 + - - +
145B ILE 3.4 3.1 + - - -
146B ALA 4.0 0.5 + - - -
152B THR* 2.9 43.1 + - + +
153B ASN* 5.3 1.1 - - - -
155B ALA* 3.7 18.6 - - + +
156B THR* 2.6 36.3 + - - +
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Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A MET* 4.4 1.4 - - - +
109A THR* 3.5 24.8 - - + +
112A ALA* 2.9 31.1 - - + +
113A ARG* 2.8 45.0 - - - +
116A ARG* 3.9 4.2 - - - +
117A PHE* 3.4 16.5 - - - -
38B PHE* 5.7 1.5 - - - -
58B TYR* 2.6 32.8 + - - -
140B VAL 3.2 11.3 + - - +
141B TYR* 3.1 32.8 + - + +
143B HIS* 1.3 80.5 - - - +
145B ILE* 1.3 56.8 + - + +
146B ALA 3.9 0.9 - - - -
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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