Contacts of the helix formed by residues 300 - 313 (chain B) in PDB entry 7A62
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 PRO 300 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ARG* 4.9 11.9 - - - +
120B LEU* 3.9 10.1 - - + -
127B ALA* 3.6 31.4 - - + -
131B LEU* 5.1 3.1 - - + -
268B SER* 5.2 1.3 - - - +
298B TYR 4.3 0.4 - - - +
299B MET* 1.3 88.1 - - + +
301B PRO* 1.3 76.0 - - + +
302B ALA* 4.5 3.1 - - + +
303B HIS* 2.8 40.7 + - + +
304B ARG 2.8 18.5 + - - -
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Residues in contact with PRO 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU 3.3 26.5 - - - +
119B GLU* 3.9 27.1 - - + +
120B LEU* 4.6 1.6 - - + -
299B MET 3.4 0.2 - - - -
300B PRO* 1.3 85.1 - - + +
302B ALA* 1.3 58.7 + - + +
304B ARG* 3.0 34.1 + - - +
305B ASN* 2.7 40.2 + - - +
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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
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14B ALA 5.1 1.6 - - - +
15B TYR* 3.7 29.4 - - - +
16B HIS* 3.9 28.5 - - + +
300B PRO* 3.2 3.3 - - + -
301B PRO* 1.3 81.8 - - + +
303B HIS* 1.3 60.6 + - + +
305B ASN* 3.4 8.8 + - - +
306B PHE* 3.1 24.1 + - - +
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Residues in contact with HIS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR 3.3 17.7 - - - -
16B HIS* 2.9 25.4 + - - +
17B ILE* 4.6 0.4 - - + -
23B PHE* 3.1 56.9 - + + +
77B ARG* 5.9 3.8 - - - -
131B LEU* 4.8 3.6 - - + +
268B SER* 4.0 17.2 + - - +
299B MET* 4.8 2.0 - - + -
300B PRO* 2.8 38.8 + - + +
302B ALA* 1.3 77.3 - - + +
304B ARG* 1.3 66.1 + - - +
306B PHE* 3.3 6.7 + - - +
307B LEU* 3.1 30.3 + - - +
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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
----------------------------------------------------------
119B GLU* 2.4 38.9 + - - +
296B ARG* 3.2 38.4 + - + +
297B ARG* 4.4 14.3 + - - +
299B MET* 3.3 20.2 + - + +
300B PRO 2.8 6.0 + - - +
301B PRO* 3.1 33.1 - - + +
303B HIS* 1.3 77.3 - - - +
305B ASN* 1.3 65.1 + - - +
307B LEU* 3.4 8.7 + - - +
308B CYS* 3.3 25.2 + - - +
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Residues in contact with ASN 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 3.9 14.5 - - + -
301B PRO* 2.7 30.4 + - - +
302B ALA* 3.8 8.5 - - - +
304B ARG* 1.3 73.2 - - - +
306B PHE* 1.3 67.1 + - - +
308B CYS* 3.2 6.8 + - - +
309B SER* 2.8 24.4 + - - -
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY* 3.9 23.1 - - - -
15B TYR* 3.5 33.5 - + + -
17B ILE* 3.4 32.5 - - + -
23B PHE* 4.1 13.7 - + - -
178B ILE* 4.6 2.7 - - + -
181B ILE* 4.4 13.7 - - + -
272B CYS* 3.8 17.5 - - - -
302B ALA 3.1 14.3 + - - +
303B HIS* 3.3 10.1 + - - +
305B ASN* 1.3 76.1 - - - +
307B LEU* 1.3 69.9 + - + +
309B SER* 3.1 5.3 + - - -
310B LEU* 3.0 58.8 + - + +
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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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23B PHE* 5.7 0.2 - - + -
268B SER* 4.3 9.9 - - - +
271B GLN* 4.0 13.7 - - + +
272B CYS* 3.5 38.8 - - + +
275B VAL* 4.2 8.7 - - + +
296B ARG* 3.7 37.7 - - - +
299B MET* 4.0 26.0 - - + -
303B HIS 3.1 15.1 + - - +
304B ARG* 3.8 7.0 - - - +
305B ASN 3.3 0.2 - - - -
306B PHE* 1.3 83.4 - - + +
308B CYS* 1.3 61.3 + - - +
310B LEU* 3.4 5.7 + - - +
311B GLU* 3.1 24.7 + - - +
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Residues in contact with CYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ARG* 4.1 16.8 - - - -
304B ARG 3.3 12.3 + - - +
305B ASN* 3.2 9.7 + - - +
307B LEU* 1.3 75.6 - - - +
309B SER* 1.3 68.3 + - - +
311B GLU* 3.1 22.7 + - - +
312B SER* 3.1 12.5 + - - -
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Residues in contact with SER 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TYR* 3.4 31.3 + - - -
305B ASN 2.8 13.3 + - - -
306B PHE* 3.3 10.5 + - - -
308B CYS* 1.3 76.6 - - - +
310B LEU* 1.3 54.5 + - - +
312B SER* 2.5 36.9 + - - -
313B ASN* 2.7 18.6 + - - +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 4.1 16.6 - - + -
185B PHE* 3.7 31.9 - - + -
272B CYS* 3.9 25.6 - - - +
275B VAL* 3.7 18.3 - - + +
276B LEU* 4.7 7.6 - - + +
306B PHE* 3.0 51.3 + - + +
307B LEU* 3.6 8.3 - - - +
309B SER* 1.3 79.2 - - - +
311B GLU* 1.3 63.2 + - - +
312B SER 3.0 1.0 + - - -
313B ASN* 3.3 21.3 + - - +
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 4.1 20.2 - - + +
280B GLN* 6.0 0.2 + - - -
282B THR* 3.9 15.2 + - - -
296B ARG* 3.5 27.2 + - - -
307B LEU 3.1 11.3 + - - +
308B CYS* 3.1 18.0 + - - +
310B LEU* 1.3 75.9 - - - +
312B SER* 1.3 57.2 + - - +
313B ASN 3.6 5.5 - - - +
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B CYS 3.1 9.0 + - - -
309B SER* 2.5 26.6 + - - -
311B GLU* 1.3 76.7 - - - +
313B ASN* 1.3 67.6 + - - +
314B PRO* 4.5 1.0 - - - +
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Residues in contact with ASN 313 (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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185B PHE* 3.4 46.6 - - + +
309B SER* 2.7 35.0 + - - +
310B LEU* 3.3 8.4 + - - +
311B GLU 3.9 6.8 - - - +
312B SER* 1.3 84.5 + - - +
314B PRO* 1.3 77.0 - - + +
315B SER* 3.7 1.4 + - - -
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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