Contacts of the helix formed by residues 143 - 148 (chain B) in PDB entry 3K7J
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 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B LYS* 5.1 0.7 - - - +
67B TYR* 3.3 16.0 - - - -
139B HIS* 3.5 21.0 - - - +
140B SER* 3.5 5.3 + - - -
142B GLU* 1.3 75.9 - - - +
144B LEU* 1.3 57.1 + - - +
145B HIS* 3.0 29.6 + - - +
146B TYR* 3.0 32.7 + - - +
147B GLU 4.3 0.2 + - - -
203B CO3 2.8 27.3 + - - -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 3.6 27.6 + - + +
59B LYS* 3.9 26.2 - - + +
64B SER* 3.6 26.9 - - - +
66B ARG 4.3 1.3 - - - +
67B TYR* 4.1 7.9 - - + -
142B GLU 3.8 0.6 + - - -
143B SER* 1.3 71.2 + - - +
145B HIS* 1.3 65.0 + - - +
146B TYR 3.1 0.4 - - - -
147B GLU* 3.2 19.6 + - - +
149B ARG* 3.1 67.2 + - + +
150B ALA* 4.0 15.9 - - + +
187B HIS* 5.6 0.6 - - - -
189B SER* 3.8 5.4 - - - +
190B VAL 4.3 1.3 - - - +
203B CO3 4.4 2.0 + - - -
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Residues in contact with HIS 145 (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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131B GLU* 3.5 20.2 - - + +
132B GLY 2.7 22.8 + - - +
133B TRP* 3.3 10.7 - - - -
134B ASP* 3.0 23.3 + - + -
139B HIS* 3.7 24.9 - + + +
143B SER* 3.0 15.0 + - - +
144B LEU* 1.3 79.1 - - - +
146B TYR* 1.3 60.5 + - - +
147B GLU 3.2 0.9 + - - -
148B GLY* 3.4 2.0 + - - -
150B ALA* 3.4 26.7 + - + +
151B VAL* 3.9 0.2 - - - -
152B ASP* 3.5 11.7 + - - -
187B HIS* 3.5 7.8 + + - -
203B CO3 3.2 16.2 - - - -
1001B ZN 2.1 37.5 - - - -
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Residues in contact with TYR 146 (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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67B TYR* 3.5 14.1 - - + +
70B LYS* 3.4 42.5 - - + +
71B ILE 2.9 22.8 + - - +
133B TRP* 3.2 13.3 + - - -
134B ASP* 3.2 41.8 - - + +
137B GLY* 3.4 20.4 - - - -
139B HIS* 3.0 40.0 + + - -
140B SER 3.0 19.2 + - - -
141B GLU 3.7 6.7 - - - -
143B SER* 3.0 28.5 + - - +
145B HIS* 1.3 79.5 - - - +
147B GLU* 1.3 58.6 + - - +
148B GLY 3.7 0.4 - - - -
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 3.4 13.8 - - + -
68B GLU* 2.8 44.9 + - - +
69B GLY 3.7 14.6 - - - +
71B ILE* 3.7 24.3 - - + +
77B ARG* 3.9 2.4 + - - +
81B LEU* 3.6 12.3 - - - +
104B THR* 4.1 2.8 - - - +
133B TRP* 4.3 1.3 - - - -
143B SER 4.5 2.0 - - - +
144B LEU* 3.5 18.5 - - - +
145B HIS 3.1 0.2 - - - -
146B TYR* 1.3 80.9 - - - +
148B GLY* 1.3 62.0 + - - +
149B ARG* 2.8 47.3 + - - +
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Residues in contact with GLY 148 (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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81B LEU* 3.9 12.1 - - - -
102B LEU 4.1 14.4 - - - -
103B MET* 3.4 8.1 - - - +
104B THR* 3.0 31.0 + - - +
107B CYS* 4.2 0.7 - - - +
133B TRP* 3.7 13.3 - - - -
144B LEU 3.4 2.4 + - - -
145B HIS 3.4 8.0 + - - -
147B GLU* 1.3 77.6 - - - +
149B ARG* 1.3 57.6 + - - +
150B ALA 3.6 4.0 - - - -
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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