Contacts of the helix formed by residues 163 - 179 (chain A) in PDB entry 3L49
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 VAL 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A UNL 4.4 10.5 - - - -
71A ARG* 6.0 2.0 - - - +
95A LEU* 3.8 29.4 - - + -
96A GLY* 3.9 14.1 - - - +
97A ASN* 3.8 21.5 - - - +
119A ASP* 6.1 0.7 - - + +
160A PHE* 2.9 32.1 + - + +
161A TYR 3.5 3.4 - - - +
162A SER* 1.3 76.7 - - - +
164A PRO* 1.4 72.6 - - + +
165A VAL* 4.2 13.0 - - + +
166A CYS* 3.0 9.5 + - + +
167A LYS* 3.0 18.4 + - - -
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Residues in contact with PRO 164 (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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96A GLY 4.2 7.9 - - - +
98A LEU* 4.1 19.5 - - + -
119A ASP 3.9 5.2 - - - +
120A THR* 4.3 8.1 - - + -
121A ALA* 3.7 45.3 - - + +
162A SER 3.5 9.6 - - - +
163A VAL* 1.4 88.4 - - + +
165A VAL* 1.3 62.6 + - - +
167A LYS* 3.2 11.5 + - + +
168A ILE* 3.1 28.8 + - + +
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A UNL 4.3 5.8 - - + +
95A LEU* 4.5 2.9 - - + -
119A ASP* 3.4 45.5 - - + +
121A ALA* 6.3 0.4 - - + -
130A THR* 4.1 1.6 - - - +
133A ASN* 3.6 27.0 - - - +
163A VAL* 4.2 15.7 - - + +
164A PRO* 1.3 75.5 - - - +
166A CYS* 1.3 62.7 + - - +
168A ILE* 3.5 11.8 + - + +
169A ARG* 3.0 58.2 + - - +
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Residues in contact with CYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A UNL 4.3 17.3 - - - -
158A ASN* 5.0 2.1 - - - +
160A PHE* 3.4 31.6 - - - +
161A TYR* 4.3 3.3 - - - -
163A VAL* 3.0 3.8 + - + +
165A VAL* 1.3 79.0 - - - +
167A LYS* 1.3 61.4 + - - +
169A ARG* 3.8 9.0 - - - +
170A TYR* 3.0 30.8 + - - +
224A CYS* 2.0 57.7 - - - +
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Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A TYR* 3.4 51.1 + - + +
163A VAL 3.0 6.6 + - - +
164A PRO* 3.2 15.7 - - + +
166A CYS* 1.3 76.1 - - - +
168A ILE* 1.3 58.9 + - + +
171A ASP* 3.0 59.1 + - - +
175B TYR* 3.7 12.3 - - + +
178B GLU* 5.4 3.8 - - - -
187C GLU* 3.0 26.2 + - + +
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA* 5.4 11.2 - - + -
133A ASN* 3.6 39.5 - - + +
134A TYR* 3.7 48.0 - - + +
164A PRO 3.1 19.5 + - - +
165A VAL* 3.7 9.2 - - + +
167A LYS* 1.3 76.6 - - + +
169A ARG* 1.3 64.3 + - - +
171A ASP* 3.2 2.1 + - - +
172A GLN* 3.0 30.9 + - + +
175B TYR* 3.5 15.9 - - + +
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Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A UNL 2.8 43.4 + - - -
119A ASP* 4.6 0.6 + - - -
133A ASN* 2.8 39.6 + - - +
136A ILE* 4.5 9.6 - - + +
137A GLY* 4.2 14.5 - - - +
165A VAL* 3.0 35.4 + - - +
166A CYS* 4.0 9.6 - - - +
168A ILE* 1.3 75.9 - - - +
170A TYR* 1.3 60.8 + - - +
172A GLN* 3.8 1.7 + - - +
173A MET* 3.4 16.6 + - - +
222A TRP* 3.5 22.1 - - + -
224A CYS* 2.8 29.1 + - + -
249A VAL* 3.6 20.0 - - + +
272A GLN* 3.4 18.6 + - - +
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Residues in contact with TYR 170 (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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156A VAL* 3.9 9.0 - - + -
158A ASN* 3.6 33.0 - - - +
161A TYR* 3.4 26.2 - + + -
166A CYS 3.0 19.0 + - - +
167A LYS 3.9 2.2 - - - +
169A ARG* 1.3 75.0 - - - +
171A ASP* 1.3 70.7 - - - +
173A MET* 3.3 27.7 + - + +
174A LYS* 3.0 56.6 + - + +
185A ILE* 4.7 0.6 - - + +
189A GLU* 2.6 28.8 + - - -
222A TRP* 3.6 20.8 - + + -
191C ARG* 5.5 3.1 + - - -
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Residues in contact with ASP 171 (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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161A TYR* 2.8 22.1 + - - -
167A LYS* 3.0 32.7 + - - +
168A ILE 3.7 1.3 - - - +
170A TYR* 1.3 81.2 - - - +
172A GLN* 1.3 59.7 + - - +
174A LYS* 3.4 4.9 + - - +
175A TYR* 2.9 30.8 + - - +
175B TYR* 2.5 46.4 + - + +
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Residues in contact with GLN 172 (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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133A ASN 4.3 1.3 - - - +
134A TYR* 2.6 48.6 + - - +
137A GLY* 3.6 22.7 - - - -
138A ALA* 3.6 9.9 - - + +
168A ILE* 3.0 24.7 + - + +
171A ASP* 1.3 74.8 - - - +
173A MET* 1.3 65.8 + - - +
175A TYR* 3.5 5.1 + - - +
176A VAL* 3.0 29.7 + - - +
134B TYR* 5.0 0.4 + - - -
172B GLN* 2.9 42.1 + - - -
175B TYR* 4.0 14.4 - - + -
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Residues in contact with MET 173 (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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137A GLY 4.2 1.3 + - - +
141A ALA* 3.7 23.8 - - + -
144A MET* 4.9 3.1 - - + +
154A VAL* 5.2 3.6 - - - -
156A VAL* 4.4 13.0 - - + -
169A ARG 3.4 12.4 + - - +
170A TYR* 3.3 45.9 + - + +
172A GLN* 1.3 79.5 - - - +
174A LYS* 1.3 59.8 + - - +
176A VAL* 3.4 1.6 + - - +
177A LEU* 3.0 48.6 + - + +
185A ILE* 3.8 28.5 - - + -
222A TRP* 4.0 31.0 - - + +
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Residues in contact with LYS 174 (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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170A TYR* 3.0 53.4 + - + +
171A ASP* 3.9 5.6 - - - +
173A MET* 1.3 82.7 - - + +
175A TYR* 1.3 62.5 + - - +
177A LEU* 3.3 6.8 + - + +
178A GLU* 3.2 29.1 + - + +
185A ILE* 3.7 19.7 - - + -
189A GLU* 5.0 0.9 - - - +
191C ARG* 4.6 19.0 - - - +
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Residues in contact with TYR 175 (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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171A ASP 2.9 18.0 + - - +
172A GLN* 3.8 8.5 - - - +
174A LYS* 1.3 75.8 - - - +
176A VAL* 1.3 59.8 + - - +
178A GLU* 3.2 49.5 - - - +
179A ALA* 4.0 2.6 + - - +
134B TYR* 3.6 29.8 + + - -
167B LYS* 3.5 12.4 - - + +
168B ILE* 3.4 21.7 - - + +
171B ASP* 2.6 43.6 + - + +
172B GLN* 3.6 25.1 - - - -
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Residues in contact with VAL 176 (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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138A ALA* 4.2 20.0 - - + +
141A ALA* 3.9 22.9 - - + +
142A LEU* 4.1 19.3 - - + -
145A VAL* 4.4 7.2 - - + -
172A GLN 3.0 21.5 + - - +
173A MET 3.6 3.4 - - - +
175A TYR* 1.3 75.2 - - + +
177A LEU* 1.3 68.3 + - + +
179A ALA* 3.2 15.2 + - - +
180A PHE* 3.3 13.9 - - + -
134B TYR* 3.8 40.3 + - + +
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Residues in contact with LEU 177 (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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141A ALA* 4.7 10.1 - - + +
144A MET* 5.8 5.6 - - + -
145A VAL* 5.2 5.2 - - + -
154A VAL* 4.7 8.7 - - + -
173A MET* 3.0 41.7 + - + +
174A LYS* 3.7 7.4 - - + +
175A TYR 3.3 0.2 - - - -
176A VAL* 1.3 83.4 - - + +
178A GLU* 1.3 63.8 + - - +
179A ALA 3.2 0.4 - - - -
180A PHE* 3.1 27.1 + - + +
183A VAL* 3.8 43.1 - - + +
185A ILE* 3.7 32.5 - - + +
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Residues in contact with GLU 178 (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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174A LYS* 3.2 17.4 + - + +
175A TYR* 3.2 48.3 + - - +
176A VAL 3.2 0.2 - - - -
177A LEU* 1.3 77.6 - - - +
179A ALA* 1.3 58.1 + - - +
180A PHE 3.2 3.7 + - - -
181A PRO* 4.6 4.5 - - - +
167B LYS* 5.1 5.2 + - - -
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Residues in contact with ALA 179 (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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175A TYR 4.0 1.1 + - - +
176A VAL 3.2 13.7 + - - +
177A LEU 3.2 1.0 - - - -
178A GLU* 1.3 78.2 - - - +
180A PHE* 1.3 73.0 + - + +
181A PRO* 3.4 9.7 - - - +
121B ALA* 5.5 12.2 - - + -
122B THR 5.6 1.0 - - - -
123B PRO* 4.9 9.7 - - - +
134B TYR* 4.0 17.0 - - - +
168B ILE* 6.3 0.2 - - + -
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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