Contacts of the helix formed by residues 300 - 316 (chain B) in PDB entry 4USE
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 ASN 300 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B VAL* 3.9 13.0 - - + -
140B GLN* 4.0 14.8 - - - +
168B GLU* 3.0 22.4 + - - +
169B GLY 3.6 11.5 + - - +
170B ASP* 2.9 26.4 + - - +
299B SER* 1.3 71.7 - - - +
301B LYS* 1.3 64.5 + - - +
302B ALA 3.3 2.5 - - - -
303B LEU* 3.0 7.6 + - - +
304B ARG* 3.0 38.5 + - - +
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Residues in contact with LYS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B SER* 3.3 19.9 + - - +
300B ASN* 1.3 79.1 + - - +
302B ALA* 1.3 64.8 + - - +
304B ARG* 2.9 24.9 + - - +
305B GLU* 2.9 46.6 + - + +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PRO* 3.7 40.2 - - + +
133B GLN* 3.4 22.4 + - + +
136B VAL* 4.6 6.2 - - + +
299B SER 5.1 0.2 + - - -
300B ASN 3.3 0.6 - - - -
301B LYS* 1.3 80.1 - - - +
303B LEU* 1.3 57.6 + - - +
305B GLU* 3.6 13.7 + - - +
306B LEU 3.2 18.9 + - - -
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 6.1 0.4 - - + -
129B LEU* 4.5 1.1 - - + -
133B GLN* 4.0 12.8 - - + +
136B VAL* 3.4 32.9 - - + +
137B VAL* 3.8 30.5 - - + +
140B GLN* 4.5 0.4 - - - +
165B MET* 3.8 21.5 - - + -
169B GLY* 3.5 23.6 - - - +
171B ILE* 4.4 8.7 - - + -
300B ASN 3.0 5.9 + - - +
302B ALA* 1.3 75.0 - - - +
304B ARG* 1.3 66.0 + - - +
305B GLU 3.1 1.3 - - - -
306B LEU* 3.8 26.7 - - + +
307B VAL* 3.0 29.1 + - - +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU 4.3 8.5 - - - +
168B GLU* 3.5 29.9 + - - +
169B GLY* 3.9 9.5 - - - +
299B SER* 5.7 3.2 + - - -
300B ASN* 3.0 25.0 + - - +
301B LYS* 2.9 29.4 + - - +
303B LEU* 1.3 76.5 - - - +
305B GLU* 1.3 62.7 + - + +
307B VAL* 3.5 3.8 + - - +
308B ALA* 3.2 23.1 + - + +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 5.4 1.8 - - - +
301B LYS* 2.9 45.9 + - + +
302B ALA* 3.7 12.0 - - - +
304B ARG* 1.3 76.5 - - + +
306B LEU* 1.3 63.7 + - - +
308B ALA* 3.3 7.7 + - - +
309B GLU* 3.1 36.9 + - - +
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 5.6 2.9 - - + -
121B ILE* 4.0 22.0 - - + -
125B LEU* 3.5 28.2 - - + +
127B ARG* 4.9 4.7 - - - +
128B GLY 5.5 0.9 - - - +
129B LEU* 3.7 39.3 - - + -
133B GLN* 3.4 31.1 - - + +
165B MET* 6.1 0.9 - - + -
302B ALA 3.2 11.5 + - - +
303B LEU* 3.3 17.7 + - + +
305B GLU* 1.3 72.8 - - - +
307B VAL* 1.3 67.4 + - + +
308B ALA 3.3 0.2 + - - -
309B GLU* 3.4 12.8 + - - +
310B ALA* 3.0 21.7 + - - +
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Residues in contact with VAL 307 (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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115B GLY* 4.2 14.8 - - - +
121B ILE* 4.8 4.9 - - + -
165B MET* 4.0 27.6 - - + -
166B THR 3.9 20.2 - - - +
167B LEU* 3.9 34.1 - - + +
169B GLY* 4.5 1.8 - - - -
303B LEU 3.0 22.3 + - - +
304B ARG 3.9 4.3 - - - +
305B GLU 3.3 0.2 - - - -
306B LEU* 1.3 79.4 - - + +
308B ALA* 1.3 57.4 + - - +
310B ALA* 3.4 7.8 + - + +
311B LYS* 3.1 26.1 + - + +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ARG 3.2 14.4 + - - +
305B GLU* 3.6 10.3 - - - +
306B LEU 3.2 0.6 - - - -
307B VAL* 1.3 74.8 - - - +
309B GLU* 1.3 65.7 + - + +
311B LYS* 3.3 7.3 + - - +
312B ALA* 3.1 23.9 + - - +
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Residues in contact with GLU 309 (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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125B LEU* 3.6 14.1 - - + +
127B ARG* 3.1 24.4 + - - +
133B GLN* 4.5 5.6 + - - -
305B GLU* 3.1 27.4 + - - +
306B LEU* 3.7 17.5 - - - +
308B ALA* 1.3 75.3 - - + +
310B ALA* 1.3 56.5 + - - +
312B ALA* 3.5 6.4 + - - +
313B GLU* 3.0 28.8 + - - +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLY 5.5 1.8 - - - +
121B ILE* 4.1 32.8 - - + -
124B GLU* 4.4 5.1 - - + +
125B LEU* 3.8 14.5 - - + +
306B LEU 3.0 13.6 + - - +
307B VAL* 3.6 10.8 - - + +
308B ALA 3.2 0.2 - - - -
309B GLU* 1.3 76.1 - - - +
311B LYS* 1.3 57.7 + - - +
313B GLU* 3.2 3.2 + - - +
314B VAL* 3.0 34.5 + - + +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 5.4 10.8 - - + -
307B VAL* 3.1 14.6 + - + +
308B ALA* 3.3 6.7 + - - +
310B ALA* 1.3 79.0 - - - +
312B ALA* 1.3 61.8 + - - +
314B VAL* 3.5 10.5 + - - +
315B MET* 3.4 21.5 + - - +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ALA 3.1 15.6 + - - +
309B GLU* 3.9 6.7 - - - +
311B LYS* 1.3 76.0 - - - +
313B GLU* 1.3 63.9 + - - +
315B MET* 3.1 24.5 + - + +
316B GLU* 3.2 18.0 - - - +
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU* 3.4 39.5 - - + +
125B LEU* 3.8 13.4 - - + +
309B GLU 3.0 18.3 + - - +
310B ALA 3.2 4.7 + - - +
312B ALA* 1.3 76.8 - - - +
314B VAL* 1.3 62.5 + - - +
316B GLU* 3.1 45.9 + - - +
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU* 3.5 33.9 - - + +
310B ALA* 3.0 16.4 + - + +
311B LYS* 3.7 11.7 - - - +
312B ALA 3.3 0.2 - - - -
313B GLU* 1.3 75.6 - - - +
315B MET* 1.3 62.3 + - + +
316B GLU 3.6 3.8 + - - +
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Residues in contact with MET 315 (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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311B LYS 3.4 12.5 + - - +
312B ALA* 3.1 15.8 + - + +
313B GLU 3.1 1.4 - - - -
314B VAL* 1.3 78.7 - - - +
316B GLU* 1.3 67.9 + - - +
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Residues in contact with GLU 316 (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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312B ALA* 3.2 18.7 - - - +
313B GLU* 3.1 43.6 + - - +
314B VAL 4.4 2.9 - - - +
315B MET* 1.3 84.6 - - - +
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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