Contacts of the helix formed by residues 162 - 176 (chain A) in PDB entry 4KM5
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 ALA 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A GLY* 1.3 76.3 - - - +
163A SER* 1.3 56.4 + - - +
164A LYS* 3.2 2.6 - - - +
165A LEU* 3.6 18.6 - - - +
166A ARG* 2.7 35.2 + - + +
458A LYS 5.7 2.5 - - - +
460A LEU* 3.6 26.0 - - + +
461A GLY* 3.5 24.8 - - - +
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Residues in contact with SER 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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161A GLY* 2.9 13.6 + - - -
162A ALA* 1.3 79.4 - - - +
164A LYS* 1.3 60.7 + - - +
166A ARG* 4.0 5.1 - - - +
167A ALA* 3.5 18.2 + - - +
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Residues in contact with LYS 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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162A ALA 3.2 0.6 - - - +
163A SER* 1.3 78.8 - - - +
165A LEU* 1.3 72.5 + - + +
167A ALA* 3.2 9.3 + - - +
168A VAL* 3.2 25.6 + - + +
514A ASN 4.8 1.0 + - - -
515A GLU* 2.7 41.7 + - + +
516A PHE* 2.7 24.3 + - + -
517A PRO* 3.6 8.5 - - - +
519A PHE* 4.5 2.5 - - + -
520A ASP* 3.8 35.1 + - + +
521A GLU* 5.7 2.7 - - - +
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Residues in contact with LEU 165 (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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162A ALA* 3.3 15.4 + - - +
164A LYS* 1.3 84.0 - - + +
166A ARG* 1.3 63.6 + - - +
168A VAL* 3.0 16.0 + - - +
169A LEU* 3.1 20.9 + - - +
412A LEU* 4.0 26.0 - - + +
460A LEU* 4.0 7.9 - - + +
461A GLY* 3.7 30.1 - - - +
464A PHE* 4.0 27.1 - - + -
516A PHE* 5.0 7.6 - - + -
519A PHE* 4.2 26.7 - - + -
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Residues in contact with ARG 166 (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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162A ALA* 2.7 22.9 + - - +
163A SER* 4.0 6.1 - - - +
165A LEU* 1.3 73.3 - - - +
167A ALA* 1.3 63.6 - - - +
169A LEU* 3.2 13.5 + - - +
170A GLU* 3.1 47.6 + - + +
173A LYS* 5.5 3.4 - - - +
408A ASP* 3.7 8.7 + - - -
457A ARG* 3.1 51.0 + - - +
460A LEU* 3.3 27.5 - - - +
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Residues in contact with ALA 167 (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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163A SER 3.5 11.2 + - - +
164A LYS* 3.2 12.7 + - - +
165A LEU 3.2 0.4 - - - -
166A ARG* 1.3 79.9 - - - +
168A VAL* 1.3 62.5 + - - +
170A GLU* 3.5 14.8 + - - +
171A LYS* 3.6 13.7 + - - +
520A ASP* 3.7 15.5 - - - +
521A GLU* 6.1 1.8 - - - +
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Residues in contact with VAL 168 (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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164A LYS* 3.2 17.0 - - + +
165A LEU* 3.0 13.4 + - - +
167A ALA* 1.3 75.2 - - - +
169A LEU* 1.3 65.2 + - - +
171A LYS* 3.1 18.5 - - - +
172A LEU* 3.1 31.4 - - + +
412A LEU* 3.8 20.4 - - + -
415A TYR* 3.9 23.1 - - + -
519A PHE* 4.0 22.9 - - + -
520A ASP* 3.9 20.9 - - + -
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Residues in contact with LEU 169 (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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165A LEU 3.1 29.8 + - - +
166A ARG* 3.2 16.4 + - - +
168A VAL* 1.3 79.5 - - - +
170A GLU* 1.3 60.7 + - - +
172A LEU* 3.5 16.6 + - + +
173A LYS* 3.3 35.5 + - - +
176A ARG* 5.0 2.2 + - - +
408A ASP* 3.6 30.7 - - + +
411A LYS* 4.3 18.2 - - + -
412A LEU* 3.8 35.4 - - + -
460A LEU* 4.1 13.7 - - + -
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Residues in contact with GLU 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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166A ARG* 3.1 37.6 + - + +
167A ALA* 3.8 10.1 - - - +
168A VAL 3.1 0.4 - - - -
169A LEU* 1.3 77.9 - - - +
171A LYS* 1.3 58.6 + - - +
173A LYS* 3.2 42.7 + - - +
174A LEU* 3.5 19.2 - - + +
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Residues in contact with LYS 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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167A ALA 3.6 8.4 + - - +
168A VAL* 3.1 24.4 + - - +
170A GLU* 1.3 78.1 - - - +
172A LEU* 1.3 72.3 + - + +
173A LYS 3.3 0.8 + - - -
174A LEU* 3.6 17.7 + - + +
175A SER* 3.7 12.1 + - - -
415A TYR* 3.7 13.9 + - - -
519A PHE 3.2 14.2 + - - -
520A ASP* 2.6 30.4 + - - +
521A GLU 3.9 2.6 + - - +
522A PHE* 3.5 31.9 - - + +
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Residues in contact with LEU 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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168A VAL* 3.1 34.0 + - + +
169A LEU* 3.5 21.5 + - + +
170A GLU 3.4 0.2 - - - -
171A LYS* 1.3 87.3 - - + +
173A LYS* 1.3 58.8 + - - +
175A SER* 2.7 21.3 + - - +
176A ARG* 3.7 21.4 + - - +
220A ILE* 3.6 41.5 - - + +
221A SER* 5.7 0.7 - - - -
411A LYS* 5.1 5.6 - - + -
412A LEU* 5.1 1.3 - - + -
415A TYR* 4.3 25.1 - - + +
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Residues in contact with LYS 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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166A ARG* 5.5 4.2 - - - +
169A LEU* 3.3 21.3 + - - +
170A GLU* 3.2 51.7 + - - +
172A LEU* 1.3 76.3 - - - +
174A LEU* 1.3 67.9 + - + +
175A SER 3.0 2.0 - - - -
176A ARG* 3.0 52.5 + - + +
177A ASP* 3.2 13.2 - - - +
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Residues in contact with LEU 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 GLU* 3.5 19.3 + - + +
171A LYS* 3.6 12.7 + - + +
172A LEU 3.4 0.4 - - - -
173A LYS* 1.3 87.1 - - + +
175A SER* 1.3 59.2 + - - +
176A ARG 3.8 0.2 + - - -
177A ASP* 4.1 11.7 + - + +
178A ASP* 4.2 8.3 + - - +
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Residues in contact with SER 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 LYS 3.7 8.3 + - - -
172A LEU* 2.7 27.5 + - - +
174A LEU* 1.3 80.1 - - - +
176A ARG* 1.3 58.3 + - - +
177A ASP 3.3 1.3 - - - -
178A ASP* 3.5 11.9 + - - +
179A ILE* 3.2 24.5 + - - +
220A ILE 5.1 5.7 + - - -
223A PRO* 4.1 21.5 - - - +
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Residues in contact with ARG 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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169A LEU* 5.0 2.8 + - - +
172A LEU* 3.9 14.7 + - - +
173A LYS* 3.0 51.5 + - - +
175A SER* 1.3 79.1 + - - +
177A ASP* 1.3 66.7 + - - +
178A ASP 3.3 0.7 - - - -
179A ILE* 3.4 33.2 - - + +
180A SER* 3.9 5.0 + - - -
214A TYR* 4.1 27.8 + - + +
411A LYS* 3.4 37.3 - - - +
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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