Contacts of the helix formed by residues 149 - 163 (chain A) in PDB entry 1UMD
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 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A PHE* 3.3 36.7 - - + -
93A PRO 3.4 14.9 + - - +
94A TYR* 4.1 15.5 - - + -
140A PHE* 4.9 5.8 - - + -
142A VAL* 6.6 0.2 - - - -
143A ALA* 5.5 8.5 + - + +
145A PRO 4.9 1.8 + - - -
147A ALA* 3.8 24.7 + - - -
148A SER* 1.3 79.6 + - - +
150A VAL* 1.3 64.7 + - + +
152A PRO* 3.4 9.3 - - - +
153A ALA* 3.1 22.7 + - - +
171A CYS* 3.8 9.8 - - - -
172A THR 2.8 26.6 + - - -
173A PHE* 4.3 9.2 - - + -
97B GLN* 3.8 13.0 - - - +
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Residues in contact with VAL 150 (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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147A ALA* 3.0 23.4 + - + +
149A HIS* 1.3 78.1 - - + +
151A PRO* 1.3 74.0 - - + +
153A ALA* 3.1 4.5 + - - +
154A ALA* 3.1 19.9 + - - +
171A CYS* 4.0 18.6 - - - -
173A PHE* 4.4 6.1 - - + -
182A ASP 4.1 3.1 - - - +
183A TRP* 3.6 42.4 - - + +
187A ILE* 3.8 23.6 - - + +
199A PHE* 3.9 11.3 - - + -
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Residues in contact with PRO 151 (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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147A ALA 3.6 9.9 - - - +
148A SER 3.7 3.4 - - - +
150A VAL* 1.3 95.2 - - + +
152A PRO* 1.3 72.8 - - + +
154A ALA* 3.1 5.8 + - + +
155A GLY 2.9 17.2 + - - -
182A ASP* 3.4 24.0 - - + +
186A GLY* 4.0 17.5 - - - +
61B ALA 3.7 24.7 - - - +
62B ALA* 4.6 2.0 - - - +
65B GLY* 3.8 10.5 - - - -
66B ALA* 3.5 8.4 - - - +
93B GLN* 3.6 13.5 - - - +
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Residues in contact with PRO 152 (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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92A PHE* 3.9 13.2 - - + -
140A PHE* 4.2 4.9 - - + -
148A SER 3.1 24.7 - - - +
149A HIS 3.4 10.1 - - - +
151A PRO* 1.3 95.2 - - + +
153A ALA* 1.3 56.3 + - - +
155A GLY 3.1 0.5 + - - -
156A ALA* 2.9 29.3 + - - +
65B GLY 3.2 16.6 - - - +
68B LEU* 4.0 19.5 - - + -
69B GLY* 3.3 9.7 - - - -
93B GLN* 3.5 11.0 - - - +
97B GLN* 4.0 13.9 - - + -
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Residues in contact with ALA 153 (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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92A PHE* 3.7 29.5 - - + -
149A HIS 3.1 14.8 + - - +
150A VAL 3.1 11.0 + - - +
152A PRO* 1.3 74.9 - - - +
154A ALA* 1.3 62.8 + - - +
156A ALA* 3.4 2.6 + - - +
157A ALA* 3.1 22.9 + - - +
169A ALA* 4.0 8.1 - - + +
171A CYS* 3.7 24.9 - - + -
197A ALA* 4.6 2.4 - - - +
199A PHE* 4.4 4.7 - - + -
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Residues in contact with ALA 154 (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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150A VAL 3.1 9.7 + - - +
151A PRO* 3.1 10.7 + - + +
153A ALA* 1.3 78.0 - - - +
155A GLY* 1.3 61.3 + - - +
157A ALA* 3.3 6.5 + - - +
158A ILE* 3.0 31.3 + - + +
186A GLY* 3.5 26.5 - - - +
189A PHE* 5.2 2.7 - - + -
190A ALA* 3.7 21.8 - - + +
195A ALA* 4.4 0.7 - - - +
199A PHE* 4.5 4.8 - - + -
66B ALA* 5.2 3.1 - - + -
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Residues in contact with GLY 155 (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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151A PRO 2.9 11.3 + - - -
152A PRO 3.1 1.8 + - - -
154A ALA* 1.3 74.5 - - - +
156A ALA* 1.3 63.6 + - - +
158A ILE* 3.2 4.6 + - - +
159A SER* 3.0 18.7 + - - -
66B ALA* 3.2 34.2 - - - +
70B MET* 3.3 19.5 - - - +
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Residues in contact with ALA 156 (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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90A TRP* 4.8 2.9 - - + -
92A PHE* 3.5 35.7 - - + -
152A PRO 2.9 8.2 + - - +
153A ALA 3.8 2.9 - - - +
155A GLY* 1.3 75.0 - - - +
157A ALA* 1.3 56.4 + - - +
159A SER* 3.2 4.2 + - - -
160A MET* 2.9 41.5 + - + +
169A ALA* 4.7 0.4 - - + -
69B GLY 3.6 18.4 - - - +
73B HIS* 4.1 12.9 - - + -
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Residues in contact with ALA 157 (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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153A ALA 3.1 13.9 + - - +
154A ALA 3.5 8.5 - - - +
155A GLY 3.2 0.2 - - - -
156A ALA* 1.3 73.4 - - - +
158A ILE* 1.3 65.4 + - - +
160A MET* 3.2 12.9 + - - -
161A LYS 3.0 18.5 + - - -
169A ALA* 4.2 2.6 - - + +
195A ALA* 3.8 7.2 - - + -
196A PRO* 3.2 39.1 - - - +
197A ALA* 3.7 16.6 - - + -
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Residues in contact with ILE 158 (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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154A ALA* 3.0 21.0 + - + +
155A GLY* 3.2 7.4 + - - +
157A ALA* 1.3 75.4 - - - +
159A SER* 1.3 57.2 + - - +
161A LYS* 3.2 8.4 + - + +
162A LEU* 2.9 36.2 + - + +
189A PHE* 3.5 44.0 - - + +
190A ALA* 5.2 0.2 - - - -
193A GLN* 4.0 18.8 - - + +
195A ALA* 3.8 18.4 - - + -
54B MET* 4.0 16.8 - - + -
70B MET* 3.4 24.5 - - + -
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Residues in contact with SER 159 (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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155A GLY 3.0 13.1 + - - -
156A ALA 3.3 9.0 - - - -
157A ALA 3.2 0.2 - - - -
158A ILE* 1.3 77.6 - - - +
160A MET* 1.3 56.2 + - - +
162A LEU* 3.3 1.0 + - - +
163A LEU* 2.8 39.8 + - - +
70B MET* 4.1 5.4 - - - -
73B HIS* 2.8 30.7 + - - -
75B LEU* 3.3 40.4 + - - +
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Residues in contact with MET 160 (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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90A TRP* 3.5 42.8 - - + -
156A ALA* 2.9 21.2 + - + +
157A ALA* 3.4 13.2 - - - +
159A SER* 1.3 75.4 - - - +
161A LYS* 1.3 57.9 + - - +
163A LEU 3.8 0.2 - - - -
164A ARG* 3.0 22.9 + - - -
165A THR* 3.2 23.3 + - - +
166A GLY 4.4 2.1 + - - -
167A GLN* 3.6 26.5 - - + +
168A VAL* 3.6 34.3 - - - +
169A ALA* 3.7 9.6 - - + -
196A PRO* 4.2 2.5 - - + +
73B HIS* 3.6 21.3 - - + +
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Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ALA 3.0 12.9 + - - +
158A ILE* 3.5 11.9 - - + +
159A SER 3.2 0.2 - - - -
160A MET* 1.3 76.8 - - - +
162A LEU* 1.3 74.9 + - + +
164A ARG* 3.2 18.9 + - - +
193A GLN* 2.7 38.1 + - + +
194A GLY* 4.2 12.9 + - - +
195A ALA* 4.7 2.2 - - - -
196A PRO* 3.9 13.4 - - + +
51B ASP* 5.4 5.6 + - - -
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A ILE* 2.9 25.1 + - + +
159A SER 3.9 2.7 - - - +
161A LYS* 1.3 87.6 - - + +
163A LEU* 1.3 65.4 + - + +
164A ARG* 3.2 6.6 + - - +
193A GLN* 5.9 1.6 - - - +
25B VAL* 4.7 4.7 - - + -
51B ASP* 3.4 56.1 - - + +
54B MET* 3.6 24.0 - - + -
75B LEU* 3.9 27.4 - - + -
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Residues in contact with LEU 163 (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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159A SER* 2.8 35.2 + - - +
162A LEU* 1.3 77.0 - - - +
164A ARG* 1.3 70.5 + - - +
165A THR* 3.2 16.6 + - + +
22B PRO 6.0 1.3 - - - +
23B ARG* 5.1 10.1 - - + -
73B HIS* 4.1 13.0 - - + +
74B GLY* 4.2 15.3 - - - +
75B LEU* 3.9 24.9 - - + -
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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