Contacts of the helix formed by residues 157 - 170 (chain B) in PDB entry 4K71
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 PHE 157 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLN* 5.5 9.0 - - + -
81A ARG 3.5 19.7 - - - +
82A GLU 3.4 17.7 - - - -
83A THR 3.4 20.9 - - - -
84A TYR 4.4 1.1 - - - -
85A GLY* 3.6 22.2 - - - -
153B THR* 2.9 18.6 + - + +
156B LEU* 1.3 78.3 - - - +
158B SER* 1.3 80.7 + - - +
159B CYS 3.4 1.7 + - - -
160B PRO* 3.4 1.6 - - - +
161B HIS* 3.0 55.7 + + + +
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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
----------------------------------------------------------
67B ASP* 4.5 5.0 + - - -
153B THR* 2.8 23.4 + - - +
154B PHE* 3.7 13.3 - - - -
157B PHE* 1.3 87.6 - - - +
159B CYS* 1.3 58.0 + - - +
161B HIS* 3.8 3.2 - - - +
162B ARG* 2.8 65.1 + - - +
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Residues in contact with CYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.4 27.9 - - + +
9B TYR* 4.9 7.4 - - + -
95B GLY* 3.6 8.5 - - - -
96B CYS* 2.1 55.6 - - + -
154B PHE* 2.9 21.4 + - + +
155B LEU* 3.8 7.4 - - - +
158B SER* 1.3 77.3 - - - +
160B PRO* 1.3 60.8 - - + +
162B ARG* 4.5 3.1 - - - +
163B LEU* 2.9 29.5 + - - +
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Residues in contact with PRO 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B CYS* 3.8 7.9 - - - -
98B LEU* 4.3 4.5 - - + -
104B SER* 3.6 33.4 - - - +
155B LEU 3.3 18.4 - - - +
156B LEU 3.6 19.3 - - - +
157B PHE 3.4 10.5 - - - +
159B CYS* 1.3 87.9 - - + +
161B HIS* 1.3 59.5 + - - +
163B LEU* 3.7 3.7 - - + +
164B ARG* 3.0 54.1 + - - +
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Residues in contact with HIS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 4.7 14.0 + - - -
82A GLU 3.4 24.8 + - - -
83A THR* 4.7 4.1 + - - +
111A ASN* 6.5 0.7 - - + -
157B PHE* 3.0 55.9 + + + +
158B SER* 3.8 4.5 - - - +
160B PRO* 1.3 78.7 - - - +
162B ARG* 1.3 63.6 + - - +
164B ARG* 3.5 21.4 + - - +
165B GLU* 3.0 34.3 + - + +
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.6 13.5 - - + -
9B TYR* 3.3 25.5 + - - -
60B TYR* 3.8 25.6 + - + +
63B LYS* 3.5 34.4 + - - +
64B GLU* 3.4 25.2 + - - +
67B ASP* 2.8 29.7 + - - -
154B PHE* 3.6 13.5 - - - -
158B SER* 2.8 43.0 + - - +
159B CYS* 4.9 0.8 - - - +
161B HIS* 1.3 71.9 - - + +
163B LEU* 1.3 58.6 + - - +
165B GLU* 3.3 5.8 + - - +
166B HIS* 2.9 38.3 + - - -
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.9 23.3 - - + +
6B SER* 4.3 10.3 - - - -
7B LEU* 3.8 11.0 - - + +
30B LEU* 3.7 24.5 - - + -
96B CYS* 3.8 27.4 - - - +
98B LEU* 3.3 30.1 - - + +
159B CYS 2.9 18.2 + - - +
160B PRO* 3.7 4.7 - - + +
162B ARG* 1.3 75.2 - - - +
164B ARG* 1.3 58.4 + - - +
166B HIS* 3.1 3.8 + - - +
167B LEU* 2.9 42.1 + - + +
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Residues in contact with ARG 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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82A GLU 5.5 1.2 + - - -
98B LEU* 3.6 28.1 - - + +
102B ASN* 3.2 50.3 + - - +
103B THR 3.6 13.5 + - - +
104B SER* 4.6 1.2 - - - +
160B PRO* 3.0 37.7 + - - +
161B HIS* 3.9 26.0 + - - +
163B LEU* 1.3 76.6 - - - +
165B GLU* 1.3 59.3 + - + +
167B LEU* 3.4 10.1 + - + +
168B GLU* 3.0 30.7 + - - +
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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
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111A ASN* 2.9 41.1 + - - +
56B GLN* 5.5 5.6 - - - +
60B TYR* 5.7 4.7 - - + -
161B HIS* 3.0 24.4 + - + +
162B ARG* 3.8 6.1 - - - +
164B ARG* 1.3 77.7 - - + +
166B HIS* 1.3 57.9 + - + +
168B GLU* 3.6 18.6 - - - +
169B ARG* 2.8 67.6 + - - +
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Residues in contact with HIS 166 (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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7B LEU* 5.2 0.7 - - + -
30B LEU* 3.7 36.1 - - + -
35B TYR* 3.7 19.8 - + - -
51B TRP* 3.9 8.9 - + + -
54B GLU* 2.6 39.7 + - - +
56B GLN* 3.3 15.6 + - - -
60B TYR* 2.5 32.7 + + - -
61B TRP* 5.2 1.6 - + - -
162B ARG* 2.9 30.5 + - + +
163B LEU 3.7 3.8 - - - +
165B GLU* 1.3 75.1 - - + +
167B LEU* 1.3 58.0 + - - +
170B GLY* 2.7 32.9 + - - -
174B LEU* 4.5 3.2 - - + +
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Residues in contact with LEU 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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5B LEU* 3.3 35.2 - - + +
98B LEU* 3.7 31.6 - - + -
163B LEU* 2.9 33.0 + - + +
164B ARG* 3.6 9.2 - - + +
166B HIS* 1.3 72.3 - - - +
168B GLU* 1.3 66.3 + - - +
171B ARG* 3.3 26.2 + - - +
174B LEU* 3.9 12.8 - - + +
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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
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164B ARG 3.0 17.2 + - - +
165B GLU* 3.6 20.3 - - - +
167B LEU* 1.3 80.9 - - - +
169B ARG* 1.3 66.7 + - + +
171B ARG* 3.8 10.3 + - - +
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Residues in contact with ARG 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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111A ASN* 4.8 4.9 + - - -
54B GLU* 3.8 13.6 - - + +
55B ASN* 3.0 66.7 + - + +
56B GLN* 3.8 21.3 + - - +
57B VAL* 3.1 30.5 - - - +
165B GLU* 2.8 55.2 + - - +
168B GLU* 1.3 75.7 - - + +
170B GLY* 1.3 56.3 + - - +
171B ARG 3.6 0.6 + - - -
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Residues in contact with GLY 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TRP* 3.8 19.6 - - - -
54B GLU* 3.8 3.9 + - - -
166B HIS 2.7 23.6 + - - -
169B ARG* 1.3 75.4 - - - +
171B ARG* 1.3 63.1 + - - +
172B GLY 3.2 3.6 - - - -
173B ASN* 3.0 25.6 + - - +
174B LEU* 3.4 9.0 + - - +
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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