Contacts of the helix formed by residues 155 - 164 (chain B) in PDB entry 4M6W
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 SER 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1980A PRO* 5.7 2.5 - - - -
2025A TYR* 4.5 1.7 - - - -
153B LEU 3.6 4.9 + - - -
154B LEU* 1.3 79.4 - - - +
156B GLU* 1.3 61.5 + - - +
157B PRO* 3.5 13.8 - - - +
158B SER* 3.3 35.6 + - - -
159B LEU* 3.4 14.2 + - - +
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Residues in contact with GLU 156 (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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2028A TYR* 2.9 36.4 + - + +
2030A PHE* 3.2 37.2 - - + -
154B LEU 4.0 3.5 + - - +
155B SER* 1.3 68.7 - - - +
157B PRO* 1.4 73.7 - - + +
159B LEU* 3.0 20.3 + - + +
160B LEU* 3.0 20.4 + - + +
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Residues in contact with PRO 157 (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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155B SER* 3.5 12.3 - - - +
156B GLU* 1.4 93.6 - - + +
158B SER* 1.3 55.7 + - - +
160B LEU* 3.4 13.3 + - + +
161B ARG* 3.1 38.9 + - - +
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Residues in contact with SER 158 (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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1978A SER 4.4 3.9 + - - +
1980A PRO* 3.5 27.1 - - - +
2025A TYR* 3.0 16.8 + - - -
155B SER* 3.3 22.2 + - - -
156B GLU 3.2 1.0 - - - -
157B PRO* 1.3 77.1 - - - +
159B LEU* 1.3 58.3 + - - +
161B ARG* 3.3 9.8 + - - +
162B THR* 2.8 27.2 + - - -
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Residues in contact with LEU 159 (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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2025A TYR* 3.4 50.9 - - + +
2028A TYR* 3.6 33.9 - - + +
2030A PHE* 4.1 18.2 - - + -
154B LEU* 3.7 16.4 - - + -
155B SER 3.4 1.3 + - - +
156B GLU* 3.0 20.2 + - - +
158B SER* 1.3 79.9 - - - +
160B LEU* 1.3 56.2 + - - +
162B THR* 3.4 2.4 + - - -
163B VAL* 3.0 34.3 + - - +
178B LEU* 4.8 3.8 - - + -
184B ILE* 3.7 19.0 - - + +
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Residues in contact with LEU 160 (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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2030A PHE* 5.5 5.4 - - + -
156B GLU* 3.0 18.6 + - + +
157B PRO* 3.7 12.6 - - + +
158B SER 3.3 0.2 - - - -
159B LEU* 1.3 73.0 - - - +
161B ARG* 1.3 56.9 + - - +
163B VAL* 3.4 4.4 + - - +
164B GLN* 2.8 52.6 + - - +
174B ALA* 4.3 3.6 - - + +
175B PRO* 3.9 44.6 - - + -
178B LEU* 4.0 22.0 - - + -
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Residues in contact with ARG 161 (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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1978A SER* 4.5 6.7 - - - +
157B PRO* 3.1 29.8 + - - +
158B SER* 3.4 12.8 - - - +
160B LEU* 1.3 76.2 - - - +
162B THR* 1.3 60.0 + - - +
164B GLN* 3.0 43.5 + - - +
165B GLN* 3.1 30.5 + - - +
171B LYS* 3.5 32.3 - - - +
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Residues in contact with THR 162 (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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1975A PHE* 3.5 37.4 - - + +
1978A SER* 2.7 34.3 + - - +
1979A ILE* 4.8 2.9 - - + -
2025A TYR* 2.7 28.8 + - + +
158B SER 2.8 14.7 + - - -
159B LEU* 3.6 5.8 - - - -
160B LEU 3.3 0.2 - - - -
161B ARG* 1.3 69.7 - - - +
163B VAL* 1.3 64.9 + - - +
165B GLN* 3.1 18.0 + - - +
184B ILE* 4.1 15.5 - - + -
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Residues in contact with VAL 163 (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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1975A PHE* 5.8 0.2 - - + -
159B LEU 3.0 18.0 + - - +
160B LEU 3.9 3.1 - - - +
162B THR* 1.3 71.0 - - + +
164B GLN* 1.3 58.1 + - - +
165B GLN 3.0 4.9 - - - -
166B ILE* 2.9 41.8 + - + +
169B VAL* 3.2 15.3 - - + +
174B ALA* 4.4 11.7 - - + -
177B LEU* 4.5 10.3 - - + -
178B LEU* 3.7 33.9 - - + -
184B ILE* 4.4 17.0 - - + -
187B LEU* 4.3 17.9 - - + -
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Residues in contact with GLN 164 (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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160B LEU* 2.8 39.7 + - - +
161B ARG* 3.0 40.6 + - - +
162B THR 3.3 0.4 - - - -
163B VAL* 1.3 74.6 - - - +
165B GLN* 1.3 60.9 + - - +
166B ILE 3.3 2.0 + - - +
169B VAL* 3.0 24.8 - - - +
170B GLY* 3.5 22.3 - - - +
171B LYS* 3.6 29.3 + - - +
174B ALA* 3.7 7.9 - - + +
175B PRO* 5.9 0.4 - - - +
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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