Contacts of the helix formed by residues 141 - 152 (chain B) in PDB entry 3H1J
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 GLN 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 3.7 28.0 - - + +
137B VAL* 3.1 19.1 + - + +
138B THR* 4.1 20.2 - - - +
140B LEU* 1.3 73.9 - - - +
142B PRO* 1.3 68.4 - - + +
143B GLN 3.0 0.4 - - - -
144B LEU* 3.1 22.9 + - + +
183B ILE* 3.3 8.3 - - - +
184B GLY* 2.8 53.2 + - - +
186B ILE* 2.9 39.9 + - - +
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Residues in contact with PRO 142 (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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138B THR 3.4 11.4 - - - +
139B ASP* 3.1 16.2 - - - +
140B LEU 2.7 7.5 - - - +
141B GLN* 1.3 91.7 - - + +
143B GLN* 1.3 56.2 + - - +
145B LYS* 2.9 32.4 - - + +
146B VAL* 3.4 5.9 + - - +
183B ILE* 4.8 2.5 - - + -
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Residues in contact with GLN 143 (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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282A ARG* 3.5 21.0 + - - +
283A THR* 4.8 9.3 - - - +
284A PHE 5.3 4.9 + - - -
285A GLY* 5.8 3.0 - - - -
71B LEU* 3.9 18.8 - - + -
140B LEU* 2.6 38.3 + - + +
142B PRO* 1.3 71.2 - - - +
144B LEU* 1.3 55.6 + - - +
146B VAL* 3.2 28.5 + - - +
147B ASP* 2.6 42.1 + - + +
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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
----------------------------------------------------------
67B HIS* 3.9 20.7 - - + +
68B LEU* 3.8 33.2 - - + +
71B LEU* 3.7 23.6 - - + -
141B GLN* 3.1 17.8 + - - +
143B GLN* 1.3 78.2 - - - +
145B LYS* 1.3 64.4 + - - +
147B ASP* 4.5 1.6 - - - -
148B LYS* 2.9 28.6 + - - +
178B CYS* 4.0 3.1 - - + -
183B ILE* 3.2 38.8 - - + -
184B GLY 4.3 3.4 - - - +
186B ILE* 3.9 25.6 - - + -
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Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PRO* 2.9 21.9 + - + +
144B LEU* 1.3 83.0 - - - +
146B VAL* 1.3 60.5 + - + +
148B LYS* 3.6 3.8 + - - +
149B ALA* 3.2 20.2 + - - +
180B ASP* 4.3 19.2 + - - +
183B ILE* 3.9 37.2 - - + +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 3.1 50.9 - - + +
283A THR* 4.6 9.9 - - + -
142B PRO 3.4 5.3 + - - +
143B GLN* 3.2 25.2 + - - +
145B LYS* 1.3 77.4 - - + +
147B ASP* 1.3 72.7 + - - +
148B LYS 3.0 1.8 - - - -
149B ALA* 2.8 20.4 + - - +
150B VAL* 3.2 18.5 + - + +
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Residues in contact with ASP 147 (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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283A THR* 4.8 6.2 - - + +
67B HIS* 2.7 29.4 + - - +
70B ARG* 4.4 1.7 + - - -
71B LEU* 3.9 15.9 - - + +
143B GLN* 2.6 24.6 + - + +
144B LEU 4.0 1.8 - - - +
146B VAL* 1.3 77.7 - - - +
148B LYS* 1.3 57.3 + - - +
150B VAL* 2.9 26.5 - - - +
151B ALA* 3.3 8.3 + - - +
177B TYR* 3.9 10.9 - - - -
68I ILE* 3.2 30.6 - - + +
74I ALA* 4.1 10.4 - - - +
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Residues in contact with LYS 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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67B HIS* 4.7 4.0 - - + -
144B LEU 2.9 18.5 + - - +
145B LYS* 3.6 4.5 - - - +
147B ASP* 1.3 77.0 + - - +
149B ALA* 1.3 59.4 + - - +
151B ALA* 3.2 2.0 + - - -
152B PHE* 2.9 60.2 + - + -
177B TYR* 3.8 35.2 + - + -
178B CYS 3.3 25.4 + - - +
179B PRO* 3.9 3.6 - - - +
180B ASP* 2.7 40.5 + - - +
183B ILE* 5.1 4.7 - - + -
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Residues in contact with ALA 149 (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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145B LYS 3.2 9.9 + - - +
146B VAL* 2.8 17.8 + - - +
148B LYS* 1.3 75.7 - - - +
150B VAL* 1.3 63.5 + - + +
152B PHE* 3.6 7.0 + - - +
153B GLN* 3.5 17.9 + - - +
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Residues in contact with VAL 150 (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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282A ARG* 6.3 1.6 - - + -
283A THR* 4.4 14.6 - - + -
146B VAL* 3.2 14.6 + - + +
147B ASP* 2.9 23.8 - - - +
149B ALA* 1.3 73.2 - - + +
151B ALA* 1.3 84.5 + - + +
153B GLN* 2.8 44.5 + - - +
154B SER* 4.8 0.5 + - - -
74I ALA* 4.3 22.9 - - + -
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Residues in contact with ALA 151 (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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147B ASP* 3.6 8.7 - - - +
148B LYS 3.2 7.1 + - - +
150B VAL* 1.3 84.1 - - + +
152B PHE* 1.3 60.6 + - + +
153B GLN 2.8 6.9 + - - -
154B SER* 3.2 18.0 + - - -
157B VAL* 3.3 10.2 - - + +
177B TYR* 3.5 40.6 - - + +
74I ALA* 6.5 0.4 - - + -
75I SER 5.6 0.9 - - - +
76I VAL* 4.7 15.9 - - + +
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Residues in contact with PHE 152 (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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148B LYS* 2.9 50.9 + - + +
149B ALA* 3.9 7.6 - - - +
150B VAL 3.1 0.2 - - - -
151B ALA* 1.3 79.1 - - + +
153B GLN* 1.3 63.4 + - - +
154B SER 3.1 5.7 + - - +
155B PRO* 4.5 1.6 - - - +
157B VAL* 3.6 13.4 - - + +
158B GLY* 4.0 24.2 + - - -
161B GLU* 3.9 24.0 - - + -
177B TYR* 3.8 24.9 - + - -
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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