Contacts of the helix formed by residues 126 - 141 (chain B) in PDB entry 1ULH
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 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B ARG* 3.3 33.3 + - - -
121B ALA 4.7 2.0 - - - -
122B MET* 3.1 28.5 - - + +
123B HIS* 2.9 63.6 + + - +
125B GLY* 1.3 78.6 - - - +
127B LEU* 1.3 60.8 + - + +
129B PRO* 3.1 16.5 - - - +
130B PHE* 3.1 26.2 - + + -
305B ALA* 5.3 5.4 - - + -
314B LEU* 5.3 1.8 - - + -
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B HIS 4.5 0.2 - - - +
124B VAL* 3.4 17.2 + - + +
125B GLY 3.2 0.8 - - - -
126B HIS* 1.3 79.0 - - + +
128B ILE* 1.3 56.6 + - - +
130B PHE* 3.4 4.2 + - + -
131B ILE* 2.8 46.2 + - + +
178B CYS* 4.1 16.2 - - - -
314B LEU* 3.7 30.7 - - + -
359B PHE* 4.6 7.6 - - + -
394B LEU* 4.1 32.8 - - + -
395B ILE* 5.6 1.3 - - + -
398B HIS* 3.6 35.7 - - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE* 3.3 32.5 - - + -
89B ILE* 4.3 1.6 - - + -
90B PHE* 3.9 12.1 - - + -
124B VAL 3.2 16.4 - - - +
125B GLY* 3.1 25.8 - - - +
126B HIS 3.2 0.6 - - - -
127B LEU* 1.3 76.8 - - - +
129B PRO* 1.4 69.1 - - + +
132B PHE* 3.3 9.0 + - - +
290B SER* 3.8 23.1 - - - +
291B THR 5.0 2.0 - - - +
293B PHE* 3.9 13.9 - - + +
358B PHE* 3.4 32.1 - - + -
359B PHE* 3.6 16.8 - - + -
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Residues in contact with PRO 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 4.0 14.3 - - + -
113B THR* 5.0 4.9 - - - +
125B GLY 3.7 6.1 - - - +
126B HIS* 3.1 26.9 - - - +
128B ILE* 1.4 89.1 - - + +
130B PHE* 1.3 66.1 + - + +
132B PHE* 3.4 2.9 + - - +
133B THR* 2.8 33.4 + - - -
261B PRO* 4.7 5.6 - - - +
262B CYS* 4.5 21.1 - - - -
263B ALA* 4.7 9.0 - - + +
290B SER* 5.1 2.5 - - - +
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Residues in contact with PHE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B THR* 4.0 22.0 - - + -
114B GLY 3.8 11.0 - - - -
115B ARG* 3.8 24.2 - - + -
122B MET* 5.4 3.4 - - - -
126B HIS* 3.1 32.8 - + + +
127B LEU* 3.4 6.0 + - + +
128B ILE 3.3 0.4 - - - -
129B PRO* 1.3 83.3 - - + +
131B ILE* 1.3 61.3 + - - +
133B THR* 2.9 6.8 + - - -
134B LYS 2.8 25.1 + - - -
146B ILE* 4.1 6.3 - - + -
175B ILE* 3.7 51.8 - - + -
178B CYS* 3.9 21.5 - - - -
180B PHE* 3.4 17.5 - + + -
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Residues in contact with ILE 131 (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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82B HIS* 3.7 19.4 - - + +
83B HIS* 5.2 4.3 - - + +
84B PHE* 3.5 32.8 - - + -
127B LEU* 2.8 42.3 + - + +
130B PHE* 1.3 71.3 - - - +
132B PHE* 1.3 59.6 + - - +
134B LYS* 3.6 10.6 - - + +
135B TRP* 3.1 24.3 + - - +
178B CYS* 4.5 20.2 - - + +
359B PHE* 5.0 11.2 - - + -
394B LEU* 6.3 3.8 - - + -
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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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82B HIS* 4.1 12.3 - + + -
84B PHE* 3.6 22.9 - + + -
85B LEU* 3.8 33.4 - - + -
90B PHE* 3.3 50.3 - + + -
128B ILE 3.3 16.5 + - - +
129B PRO 3.6 2.7 - - - +
130B PHE 3.1 0.4 - - - -
131B ILE* 1.3 79.7 - - - +
133B THR* 1.3 60.4 + - - +
135B TRP* 3.2 27.0 + + - +
136B LEU* 2.9 59.9 + - + +
261B PRO* 4.5 5.4 - - + -
288B LEU* 4.4 14.6 - - + -
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Residues in contact with THR 133 (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 LEU* 3.6 8.7 - - + +
113B THR* 4.3 13.9 + - + +
129B PRO 2.8 18.0 + - - -
130B PHE* 2.9 11.1 + - - -
132B PHE* 1.3 72.8 - - - +
134B LYS* 1.3 60.5 + - - +
135B TRP 3.0 1.8 - - - -
136B LEU* 3.1 8.5 + - - +
137B GLN* 2.8 29.3 + - - +
144B LEU* 3.5 42.2 - - + -
180B PHE* 3.9 4.0 - - + -
261B PRO* 3.5 24.4 - - + +
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Residues in contact with LYS 134 (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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130B PHE 2.8 13.8 + - - +
131B ILE* 3.6 12.6 - - - +
133B THR* 1.3 76.0 - - - +
135B TRP* 1.3 57.6 + - - +
137B GLN* 3.6 4.6 + - - +
138B ASP* 2.7 72.8 + - - +
178B CYS* 3.4 22.0 - - + +
179B GLY* 2.7 32.3 + - - -
180B PHE* 3.5 31.0 - - + +
181B ASP* 4.5 3.6 - - - +
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Residues in contact with TRP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 4.3 14.1 - - + -
77B THR* 5.4 1.1 - - - -
79B GLN* 5.0 1.5 - - + +
80B ARG 3.5 15.7 + - - -
81B PRO* 3.8 7.9 - - + -
82B HIS* 3.3 54.8 - - + +
85B LEU* 3.9 22.4 - - + -
131B ILE 3.1 15.2 + - - +
132B PHE* 3.3 21.8 - + - +
133B THR 3.0 0.4 - - - -
134B LYS* 1.3 77.8 - - - +
136B LEU* 1.3 93.9 + - + +
138B ASP* 3.5 6.5 + - + +
139B VAL* 3.1 58.5 + - + +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 5.8 1.1 - - + -
96B MET* 5.2 2.7 - - + -
109B PHE* 5.8 0.2 - - + -
111B LEU* 3.5 27.3 - - + +
132B PHE* 2.9 59.0 + - + +
133B THR* 3.1 5.1 + - - +
135B TRP* 1.3 94.4 - - + +
137B GLN* 1.3 66.8 + - - +
139B VAL* 4.9 0.2 - - - -
140B PHE* 3.0 59.3 + - + +
259B LEU* 4.6 7.0 - - + -
261B PRO* 4.5 10.5 - - + -
288B LEU* 4.5 8.5 - - + -
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Residues in contact with GLN 137 (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 LEU* 3.5 10.7 - - + +
133B THR 2.8 16.8 + - - +
134B LYS* 3.7 13.2 - - - +
136B LEU* 1.3 76.3 - - - +
138B ASP* 1.3 57.1 + - - +
141B ASN* 2.6 37.3 + - - +
142B VAL* 3.7 17.5 - - - +
144B LEU* 3.5 22.6 - - + +
180B PHE* 3.8 11.9 - - - +
181B ASP* 2.9 41.0 - - - +
184B LYS* 3.7 16.1 + - - +
185B THR* 3.0 18.3 + - - -
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Residues in contact with ASP 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 LYS* 2.7 52.7 + - - +
135B TRP* 4.0 6.2 - - + +
136B LEU 3.4 0.2 - - - -
137B GLN* 1.3 85.4 + - - +
139B VAL* 1.3 65.6 + - + +
140B PHE 3.4 0.7 + - - -
141B ASN* 3.6 9.9 + - - +
181B ASP* 5.8 1.0 - - - +
184B LYS* 5.6 5.3 + - - +
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Residues in contact with VAL 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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77B THR* 3.3 47.0 - - + +
79B GLN* 4.0 29.8 - - + +
103B TYR* 3.8 6.9 + - - -
135B TRP* 3.1 59.2 + - + +
136B LEU 4.5 0.9 - - - +
138B ASP* 1.3 79.4 - - + +
140B PHE* 1.3 62.4 + - + +
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Residues in contact with PHE 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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73B ILE* 4.4 13.9 - - + -
77B THR* 3.5 26.0 - - + -
96B MET* 4.6 12.3 - - + -
99B VAL* 5.6 0.9 - - + -
100B LEU* 4.1 20.6 - - + -
103B TYR* 3.5 59.0 + + + -
109B PHE* 3.6 23.8 - + + -
135B TRP* 5.3 0.2 - + - -
136B LEU* 3.0 52.2 + - + +
139B VAL* 1.3 82.1 - - + +
141B ASN* 1.3 73.5 + - - +
142B VAL* 3.7 16.5 - - + +
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Residues in contact with ASN 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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137B GLN 2.6 21.6 + - - -
138B ASP 3.6 9.7 + - - +
140B PHE* 1.3 77.6 - - - +
142B VAL* 1.3 54.8 + - - +
184B LYS* 2.7 38.1 + - - +
422B ASP* 2.6 40.5 + - - +
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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