Contacts of the helix formed by residues 169 - 178 (chain D) in PDB entry 2G4C
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 THR 169 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D GLN 3.4 13.2 + - - -
168D VAL* 1.3 83.7 - - - +
170D PHE* 1.3 55.4 + - - +
172D GLU* 3.4 16.6 + - - +
173D ASN* 2.5 44.7 + - + +
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Residues in contact with PHE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 4.1 8.1 - - + -
148D VAL* 5.2 2.0 - - + -
149D SER 5.1 0.4 - - - -
152D THR* 3.3 50.3 - - + -
153D LEU* 3.1 34.8 - - + -
156D ILE* 3.8 20.0 - - + -
167D LEU* 4.4 15.2 - - + +
168D VAL 3.4 0.8 - - - +
169D THR* 1.3 75.0 - - - +
171D LEU* 1.3 70.4 + - + +
172D GLU 2.7 7.4 + - - -
173D ASN* 3.0 10.9 + - - -
174D VAL* 2.7 53.7 + - + +
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Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 3.6 32.5 - - + -
156B ILE* 4.4 15.9 - - + -
157B LEU* 3.3 28.1 - - + +
167B LEU* 5.1 12.1 - - + +
170B PHE* 4.0 18.4 - - + -
171B LEU* 4.1 20.9 - - + -
167D LEU* 5.3 5.4 - - + -
168D VAL* 4.3 9.5 - - - +
170D PHE* 1.3 98.6 - - + +
172D GLU* 1.3 54.8 + - - +
174D VAL* 3.9 7.8 - - + +
175D LEU* 3.1 28.8 - - - +
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Residues in contact with GLU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LEU* 4.0 13.7 - - + -
168D VAL* 2.9 19.6 + - - +
169D THR* 3.4 26.8 + - - +
170D PHE 2.7 1.2 + - - -
171D LEU* 1.3 76.6 - - - +
173D ASN* 1.3 60.3 + - - +
174D VAL 2.9 9.7 + - - -
175D LEU* 3.3 16.1 + - - +
176D LYS* 4.0 6.8 + - - +
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Residues in contact with ASN 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D THR* 2.5 29.2 + - + +
170D PHE* 3.9 12.9 + - - +
172D GLU* 1.3 75.1 - - - +
174D VAL* 1.3 58.1 + - - +
176D LYS* 3.3 10.3 + - - +
177D THR* 2.8 54.9 + - - +
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Residues in contact with VAL 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 3.4 28.9 - - + -
148D VAL* 4.3 18.4 - - + -
170D PHE* 2.7 57.8 + - + +
171D LEU* 3.9 12.1 - - + +
172D GLU 2.9 2.0 + - - -
173D ASN* 1.3 70.1 - - - +
175D LEU* 1.3 55.7 + - - +
176D LYS 2.7 15.5 + - - -
177D THR* 3.2 2.2 + - - -
178D SER* 2.7 43.7 + - - +
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ALA* 4.2 13.2 - - + +
153B LEU* 3.3 39.3 - - + -
154B ARG* 5.1 12.1 - - + +
157B LEU* 4.7 6.3 - - + -
138D LEU* 3.3 15.8 - - - +
140D PRO* 3.9 19.4 - - + +
141D GLY* 4.4 12.8 - - - +
146D ARG* 3.6 46.2 + - + +
171D LEU 3.1 23.8 - - - +
172D GLU 3.3 6.4 + - - +
174D VAL* 1.3 72.5 - - - +
176D LYS* 1.3 59.4 + - - +
178D SER 4.7 0.2 - - - +
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Residues in contact with LYS 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLY 3.8 1.2 - - - +
137D PRO* 3.6 22.0 - - + +
138D LEU 3.3 35.7 + - - +
139D LEU* 5.5 0.4 - - - +
140D PRO* 3.7 30.0 - - + +
172D GLU 4.0 4.0 + - - +
173D ASN* 3.3 17.4 + - - +
174D VAL 2.7 4.9 + - - -
175D LEU* 1.3 75.6 - - - +
177D THR* 1.3 63.9 + - - +
178D SER 3.3 3.4 + - - +
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Residues in contact with THR 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLY* 4.0 11.3 + - - +
137D PRO* 5.5 0.9 - - - -
173D ASN* 2.8 47.6 + - - +
174D VAL* 4.3 2.0 - - - -
176D LYS* 1.3 73.6 - - - +
178D SER* 1.3 61.4 + - - +
179D GLY* 3.8 1.0 + - - -
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Residues in contact with SER 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLY 4.8 0.2 - - - -
138D LEU* 3.7 16.9 - - - +
146D ARG* 2.9 43.7 + - - +
147D LEU 3.3 15.2 + - - -
148D VAL* 4.3 2.0 + - - -
174D VAL* 2.7 36.6 + - - +
176D LYS 3.9 3.1 - - - +
177D THR* 1.3 76.5 - - - +
179D GLY* 1.3 63.6 + - - +
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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