Contacts of the helix formed by residues 300 - 307 (chain B) in PDB entry 5M7R
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 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259B ILE 4.7 3.4 + - - -
260B PRO* 6.5 0.2 - - - -
261B VAL* 4.8 8.1 - - - -
298B GLY 4.1 1.4 + - - -
299B ARG* 1.3 75.3 - - - +
301B THR* 1.3 63.1 + - - +
302B GLU* 3.0 29.3 + - - +
303B LEU* 3.0 30.7 + - - +
331B TRP* 3.8 3.9 - - - -
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Residues in contact with THR 301 (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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299B ARG 3.6 1.4 + - - -
300B SER* 1.3 72.5 + - - +
302B GLU* 1.3 63.3 + - - +
303B LEU 3.1 1.5 + - - -
304B ILE* 3.3 15.7 + - + +
331B TRP* 3.8 19.5 - - + +
334B SER* 3.1 27.8 - - - +
335B ASN* 2.9 37.8 + - + -
373B LEU* 4.2 17.7 + - + +
374B TYR* 3.9 19.6 + - + +
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Residues in contact with GLU 302 (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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261B VAL* 4.2 15.0 - - + -
300B SER* 3.0 16.1 + - - +
301B THR* 1.3 78.6 + - - +
303B LEU* 1.3 61.3 + - - +
304B ILE 3.2 0.4 - - - -
305B PRO* 3.2 15.7 - - - +
306B ARG* 3.6 16.8 - - - -
335B ASN* 4.7 5.4 + - - +
339B VAL 4.3 5.0 - - - +
340B ARG 4.2 21.1 - - - +
373B LEU* 5.7 4.7 - - - +
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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
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259B ILE* 3.4 30.7 - - + +
261B VAL* 4.0 20.9 - - + +
264B ILE* 3.7 30.3 - - + -
277B ILE* 5.4 1.3 - - + -
299B ARG* 3.8 18.4 - - + -
300B SER* 3.0 34.9 + - - +
302B GLU* 1.3 76.3 - - - +
304B ILE* 1.3 67.7 + - - +
305B PRO 3.4 0.2 - - - -
306B ARG* 2.8 20.7 + - + +
307B LEU* 3.2 30.7 + - + +
331B TRP* 4.5 6.1 - - + -
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Residues in contact with ILE 304 (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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60B PHE* 3.5 26.0 - - + -
301B THR* 3.6 16.6 - - + +
302B GLU 3.2 0.4 - - - -
303B LEU* 1.3 77.8 - - - +
305B PRO* 1.4 71.1 - - + +
307B LEU* 3.2 21.1 + - - +
331B TRP* 3.5 55.6 - - + +
332B TYR* 4.1 14.4 - - + +
335B ASN* 3.5 32.8 - - + +
336B MET 4.4 9.6 - - - +
338B GLY 5.8 0.4 - - - +
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Residues in contact with PRO 305 (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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301B THR 3.9 3.1 - - - +
302B GLU* 3.2 23.8 - - - +
304B ILE* 1.4 95.8 - - + +
306B ARG* 1.3 56.7 + - - +
307B LEU 3.3 5.1 + - - +
335B ASN* 4.1 6.7 - - - +
338B GLY* 3.8 31.2 - - - +
339B VAL* 3.9 8.7 - - - +
340B ARG* 4.0 20.9 - - - +
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Residues in contact with ARG 306 (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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261B VAL* 4.6 19.4 - - - +
264B ILE* 3.8 19.7 - - + +
265B GLU* 2.8 39.7 + - + -
268B SER* 4.4 1.6 + - - -
274B ALA* 3.3 19.8 - - - +
302B GLU* 3.6 21.1 - - - -
303B LEU* 2.8 18.8 + - + +
305B PRO* 1.3 73.5 - - - +
307B LEU* 1.3 62.5 + - - +
340B ARG* 3.4 49.6 - - - +
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Residues in contact with LEU 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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60B PHE* 3.3 13.6 - - + -
264B ILE* 4.0 11.9 - - + -
274B ALA* 4.0 6.3 - - - -
275B PRO* 3.5 29.2 - - + +
277B ILE* 3.3 36.3 - - + -
303B LEU* 3.3 38.4 - - + +
304B ILE* 3.2 18.2 + - - +
305B PRO 3.3 4.1 + - - +
306B ARG* 1.3 84.0 - - - +
308B LYS* 1.3 59.4 + - - +
309B GLY 4.0 7.4 - - - +
310B VAL* 4.1 17.7 - - + -
331B TRP* 4.9 1.3 - - + -
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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