Contacts of the helix formed by residues 159 - 178 (chain B) in PDB entry 4XZC
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 PRO 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LYS* 4.0 15.5 - - + +
158B VAL* 1.3 90.7 - - + +
160B GLY* 1.3 65.9 + - - +
161B GLU* 3.1 21.6 + - + +
162B TYR* 3.1 10.3 + - + +
163B ALA 3.1 13.0 + - - -
421B THR* 5.6 6.1 - - + +
424B GLY* 3.5 30.7 - - - +
425B ASN* 3.9 19.1 - - + +
429B LYS* 5.3 1.6 - - + -
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Residues in contact with GLY 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LYS* 4.8 2.4 - - - +
158B VAL 3.5 1.8 + - - -
159B PRO* 1.3 70.9 - - - +
161B GLU* 1.3 62.3 + - - +
162B TYR 3.2 0.9 + - - -
163B ALA* 3.3 21.7 + - - +
164B VAL* 4.0 7.8 + - - +
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B PRO* 4.1 13.1 - - + +
160B GLY* 1.3 76.7 - - - +
162B TYR* 1.3 88.6 + - + +
164B VAL* 3.6 14.8 - - - +
165B GLU* 4.6 6.8 - - - +
429B LYS* 4.7 7.4 - - - -
436B ARG* 4.9 3.3 + - - +
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Residues in contact with TYR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 3.8 15.5 - - + -
159B PRO* 3.1 9.6 + - + -
161B GLU* 1.3 104.5 + - + +
163B ALA* 1.3 58.6 + - - +
164B VAL 3.0 2.9 - - - -
165B GLU* 2.8 9.1 + - - +
166B VAL* 2.8 33.9 + - - +
428B ALA 5.4 0.4 - - - +
429B LYS* 3.4 56.0 - - + +
432B VAL* 3.4 37.7 - - + -
433B GLN* 4.3 10.0 + - + -
436B ARG* 3.2 26.6 + - - -
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 3.9 19.9 - - + +
159B PRO 3.1 13.2 + - - +
160B GLY* 3.3 18.8 + - - +
162B TYR* 1.3 76.3 - - - +
164B VAL* 1.3 60.5 + - - +
166B VAL* 3.9 4.0 - - - +
167B LYS* 3.2 42.2 + - - +
481B GLU* 4.8 5.8 - - + +
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLY 4.0 6.0 + - - +
161B GLU* 3.6 20.2 - - - +
163B ALA* 1.3 75.7 - - - +
165B GLU* 1.3 69.0 + - + +
167B LYS* 3.6 8.8 + - - +
168B GLU* 3.2 22.0 + - - +
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU 4.6 5.4 - - - +
162B TYR 2.8 6.1 + - - +
164B VAL* 1.3 86.6 - - + +
166B VAL* 1.3 59.9 + - - +
167B LYS 3.2 1.8 - - - -
168B GLU* 3.1 15.4 + - - +
169B MET* 2.9 35.7 + - - +
432B VAL* 3.5 16.1 - - + +
435B PHE* 4.2 5.9 - - + -
436B ARG* 2.8 49.5 + - - +
439B LYS* 3.2 25.3 + - - +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TYR* 4.9 4.3 - - + -
158B VAL* 3.5 34.3 - - + -
162B TYR* 2.8 29.3 + - + +
163B ALA* 3.9 7.0 - - - +
165B GLU* 1.3 72.0 - - - +
167B LYS* 1.3 57.7 + - - +
169B MET* 3.5 13.0 + - - +
170B LEU* 3.0 28.1 + - + +
428B ALA* 4.9 5.8 - - + -
432B VAL* 4.2 11.2 - - + +
456B LEU* 4.1 21.6 - - + +
460B LEU* 5.9 1.1 - - + -
481B GLU 4.0 18.6 - - - +
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Residues in contact with LYS 167 (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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163B ALA* 3.2 27.9 + - - +
164B VAL* 3.9 7.4 - - - +
165B GLU 3.2 0.6 - - - -
166B VAL* 1.3 76.8 - - - +
168B GLU* 1.3 54.7 + - - +
169B MET 3.2 0.2 - - - -
170B LEU* 3.5 14.3 - - + +
171B SER* 2.6 38.5 + - - -
481B GLU* 4.0 38.7 - - - +
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Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B VAL 3.2 14.7 + - - +
165B GLU* 3.1 14.2 + - - +
167B LYS* 1.3 77.1 - - - +
169B MET* 1.3 62.6 + - - +
171B SER* 3.7 7.3 - - - -
172B ASP* 3.1 22.2 + - + +
435B PHE* 3.9 16.9 - - + -
439B LYS* 3.5 33.8 + - - +
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Residues in contact with MET 169 (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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165B GLU 2.9 20.5 + - - +
166B VAL* 3.5 11.4 - - - +
168B GLU* 1.3 76.2 - - - +
170B LEU* 1.3 55.8 + - - +
172B ASP* 2.8 25.6 + - - +
173B MET* 2.8 17.5 + - - +
431B ILE* 3.8 25.1 - - + -
432B VAL* 4.5 11.4 - - - -
435B PHE* 3.4 53.8 - - + -
452B SER* 3.8 13.2 - - - +
453B GLU* 3.7 23.2 - - + +
456B LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 170 (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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166B VAL* 3.0 17.0 + - + +
167B LYS* 3.5 15.9 - - + +
169B MET* 1.3 78.7 - - - +
171B SER* 1.3 53.0 + - - +
173B MET* 2.9 29.4 + - + +
174B VAL* 2.7 40.9 + - + +
456B LEU* 5.3 0.7 - - + -
460B LEU* 4.7 8.3 - - + -
477B ALA 4.8 0.2 - - - +
478B THR* 4.1 30.7 - - + -
479B ASN 3.2 26.0 - - - +
480B VAL* 5.3 1.3 - - - -
481B GLU 5.5 4.9 - - - +
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LYS 2.6 21.2 + - - -
168B GLU* 3.7 9.6 - - - -
170B LEU* 1.3 74.1 - - - +
172B ASP* 1.3 56.4 + - - +
174B VAL* 3.8 10.7 - - - +
175B ARG* 3.1 27.5 + - - +
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Residues in contact with ASP 172 (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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168B GLU* 3.1 12.8 + - + +
169B MET 2.8 11.0 + - - +
171B SER* 1.3 75.9 - - - +
173B MET* 1.3 58.3 + - - +
175B ARG* 3.0 23.5 + - - +
176B ARG* 3.2 39.6 + - - +
435B PHE* 5.9 1.6 - - + -
444B LEU* 5.1 3.8 - - - +
445B ASP* 2.8 30.3 - - - +
450B VAL* 4.9 1.7 - - - +
453B GLU* 2.7 30.3 - - - +
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Residues in contact with MET 173 (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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169B MET 2.8 17.6 + - - +
170B LEU* 2.9 35.0 + - + +
172B ASP* 1.3 75.6 - - - +
174B VAL* 1.3 67.2 + - - +
175B ARG 3.2 0.2 - - - -
176B ARG* 3.3 13.1 + - - +
177B ARG* 3.5 13.9 + - - +
453B GLU* 3.5 45.3 - - + +
456B LEU* 3.6 26.0 - - + -
457B HIS* 4.4 8.5 - - - +
460B LEU* 3.7 17.7 - - + -
477B ALA* 6.4 1.8 - - + -
478B THR* 4.9 5.4 - - + -
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Residues in contact with VAL 174 (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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170B LEU* 2.7 29.3 + - + +
171B SER* 3.8 10.1 - - - +
173B MET* 1.3 73.3 - - - +
175B ARG* 1.3 60.9 + - + +
176B ARG 3.0 5.4 + - - -
177B ARG* 3.4 12.7 + - - +
178B ASN* 3.9 11.6 + - - +
478B THR* 3.6 33.7 - - + +
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Residues in contact with ARG 175 (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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171B SER 3.1 11.2 + - - +
172B ASP* 3.0 32.1 + - - +
173B MET 3.2 0.8 - - - -
174B VAL* 1.3 80.2 - - + +
176B ARG* 1.3 66.8 + - + +
178B ASN* 2.8 23.5 + - - +
179B ILE* 4.5 5.6 - - - +
445B ASP* 2.9 47.2 + - - +
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Residues in contact with ARG 176 (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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172B ASP* 3.2 35.7 + - - +
173B MET* 3.3 6.8 + - - +
174B VAL 3.0 1.2 + - - -
175B ARG* 1.3 90.1 - - + +
177B ARG* 1.3 64.9 + - - +
178B ASN 3.1 3.6 + - - -
179B ILE* 3.3 21.8 + - - +
444B LEU 3.1 33.9 + - - -
445B ASP* 3.7 9.2 - - - +
447B MET 2.7 24.6 + - - -
448B ASP 4.2 10.1 + - - -
449B ILE* 4.3 5.1 - - - +
450B VAL* 3.7 18.7 - - - +
453B GLU* 4.1 7.2 + - - -
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Residues in contact with ARG 177 (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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173B MET 3.5 8.7 + - - +
174B VAL* 3.4 9.9 + - - +
176B ARG* 1.3 77.8 - - - +
178B ASN* 1.3 57.4 + - - +
179B ILE 3.0 14.5 + - - +
296B SER* 4.8 16.3 - - - -
297B ALA* 5.1 21.4 - - - +
300B ALA* 5.8 5.7 - - - +
457B HIS* 5.1 7.3 + - - -
476B ASN* 2.5 31.7 + - - +
477B ALA* 3.2 32.4 - - - +
478B THR* 4.1 12.3 + - - +
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Residues in contact with ASN 178 (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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174B VAL* 3.9 6.9 + - - +
175B ARG* 2.8 35.0 + - - +
177B ARG* 1.3 76.5 - - - +
179B ILE* 1.3 70.5 + - - +
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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
------------------------------------------------------------
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