Contacts of the helix formed by residues 300 - 311 (chain B) in PDB entry 1AHF
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 ALA 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A ASN* 2.8 39.8 + - - +
265A GLU* 3.6 2.3 + - - +
64B GLU* 5.8 3.4 - - - +
71B LEU* 3.4 26.0 - - + -
76B ILE* 4.0 0.2 - - - +
104B GLN* 4.4 0.7 - - - +
298B PRO 3.4 0.2 + - - -
299B PRO* 1.3 74.9 - - - +
301B HIS* 1.3 66.7 + - - +
303B ALA* 3.1 5.5 + - - +
304B SER* 2.9 31.6 + - - +
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Residues in contact with HIS 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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57A GLU* 5.0 0.6 + - - -
265A GLU* 2.9 26.0 + - - +
301A HIS* 3.5 45.2 - + + +
57B GLU* 2.6 47.4 + - + +
60B LEU* 4.4 14.3 - - + +
64B GLU* 5.1 5.8 + - - -
262B LEU* 5.9 0.2 - - + -
265B GLU* 3.6 24.2 - - + +
299B PRO* 3.6 2.3 - - + +
300B ALA* 1.3 69.6 - - - +
302B GLY* 1.3 65.8 + - - +
304B SER* 2.9 17.4 + - - -
305B VAL* 2.9 25.0 + - + +
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Residues in contact with GLY 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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262B LEU* 4.5 2.9 - - - -
265B GLU* 3.7 33.8 + - - +
267B VAL* 3.7 11.9 - - - -
299B PRO* 4.8 1.2 + - - +
300B ALA 3.6 0.4 - - - -
301B HIS* 1.3 79.5 - - - +
303B ALA* 1.3 61.4 + - - +
305B VAL* 3.4 8.9 + - - +
306B VAL* 3.1 27.4 + - - +
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Residues in contact with ALA 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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76B ILE* 3.9 6.7 - - + -
79B PHE* 3.8 12.9 - - + -
104B GLN* 3.1 45.3 - - + +
265B GLU 5.6 0.2 + - - -
267B VAL* 3.8 16.5 - - + +
299B PRO 4.3 2.4 + - - +
300B ALA 3.1 5.9 + - - +
302B GLY* 1.3 77.4 - - - +
304B SER* 1.4 52.6 + - - +
306B VAL* 3.1 3.5 + - - +
307B ALA* 2.8 34.3 + - - +
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Residues in contact with SER 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.4 25.7 - - - +
64B GLU* 4.7 5.2 + - - -
76B ILE* 3.5 17.8 - - - +
300B ALA* 2.9 21.3 + - - +
301B HIS* 3.3 9.0 - - - -
303B ALA* 1.4 73.1 - - - +
305B VAL* 1.3 57.7 + - - +
307B ALA* 3.5 4.1 + - - +
308B THR* 2.5 39.4 + - - -
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Residues in contact with VAL 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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53B VAL* 4.1 21.3 - - + -
56B ALA* 3.9 18.3 - - + +
57B GLU* 3.8 26.5 - - + +
60B LEU* 3.9 12.8 - - + -
262B LEU* 3.8 24.0 - - + -
301B HIS* 2.9 26.4 + - + +
302B GLY* 3.5 9.4 - - - +
304B SER* 1.3 77.6 - - - +
306B VAL* 1.3 56.3 + - - +
308B THR* 3.7 1.4 - - - -
309B ILE* 3.1 32.6 + - + +
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Residues in contact with VAL 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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79B PHE* 4.1 18.6 - - + -
256B TYR* 4.1 13.7 - - + -
260B PHE* 3.8 35.4 - - + -
262B LEU* 3.4 23.6 - - + -
267B VAL* 4.0 11.4 - - + -
302B GLY 3.2 13.2 - - - +
303B ALA 3.1 8.8 + - - +
305B VAL* 1.3 75.6 - - - +
307B ALA* 1.3 66.9 + - - +
309B ILE* 3.4 0.7 + - - -
310B LEU* 3.0 35.6 + - + +
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Residues in contact with ALA 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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76B ILE* 4.6 9.0 - - + -
78B GLU* 4.5 7.0 - - + -
79B PHE* 4.0 30.9 - - + +
82B CYS* 4.6 6.4 - - - -
303B ALA 2.8 15.8 + - - +
304B SER* 4.0 6.1 - - - +
305B VAL 3.5 0.2 - - - -
306B VAL* 1.3 77.3 - - - +
308B THR* 1.4 55.4 + - - +
310B LEU* 3.2 1.9 + - - +
311B SER* 2.5 40.7 + - - +
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Residues in contact with THR 308 (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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56B ALA* 4.1 20.0 - - + -
59B TYR* 4.1 27.5 - - + -
60B LEU* 4.3 12.1 - - - +
304B SER* 2.5 24.6 + - - -
305B VAL* 3.7 4.4 - - - -
307B ALA* 1.4 73.8 - - - +
309B ILE* 1.3 64.9 + - - +
311B SER* 3.2 5.9 + - - -
312B ASN* 3.1 31.0 + - + +
315B LEU* 4.2 11.4 - - + -
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Residues in contact with ILE 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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52B SER* 3.7 42.0 - - - +
53B VAL* 3.8 10.8 - - + +
56B ALA* 3.9 7.0 - - + -
260B PHE* 3.7 31.9 - - + -
305B VAL* 3.1 20.6 + - + +
306B VAL 3.9 0.4 - - - +
307B ALA 3.3 0.2 - - - -
308B THR* 1.3 83.4 - - - +
310B LEU* 1.3 58.9 + - - +
312B ASN 3.3 3.3 - - - +
315B LEU* 3.9 18.1 - - + +
316B ARG* 3.2 22.7 + - - +
319B TRP* 3.5 28.7 - - + -
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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
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82B CYS* 3.8 36.1 - - + +
86B LEU* 4.3 20.4 - - + -
256B TYR* 4.5 4.3 - - + +
260B PHE* 3.8 9.6 - - + -
306B VAL* 3.0 37.1 + - + +
309B ILE* 1.3 74.0 - - - +
311B SER* 1.3 62.8 + - - +
312B ASN* 4.6 0.6 - - - -
316B ARG* 3.8 39.2 + - - +
319B TRP* 3.3 39.5 - - + -
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Residues in contact with SER 311 (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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78B GLU* 3.7 29.2 + - - +
82B CYS* 4.4 4.3 - - - -
307B ALA* 2.5 24.6 + - - +
308B THR* 3.6 6.7 - - - -
310B LEU* 1.3 79.3 - - - +
312B ASN* 1.3 59.1 + - - +
313B ASP* 3.9 4.3 + - - +
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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