Contacts of the strand formed by residues 408 - 421 (chain A) in PDB entry 1AF6
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 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A LYS* 3.3 11.6 + - - +
372A TRP* 2.9 61.1 + - - +
405A ARG 4.9 1.8 - - - -
407A ASP* 1.3 80.0 + - - +
409A ASP* 1.3 73.8 + - - +
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Residues in contact with ASP 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A TYR* 2.4 43.5 + - - -
370A ALA 3.5 3.8 - - - -
371A LYS* 3.0 18.8 - - - +
372A TRP* 3.8 7.0 - - - -
408A SER* 1.3 83.1 + - - +
410A GLU* 1.3 71.0 + - - +
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Residues in contact with GLU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 3.4 19.5 - - + +
15A GLY* 3.8 1.0 + - - -
16A SER* 2.5 45.4 + - - -
21A GLN* 4.7 6.5 + - - +
23A PHE* 3.8 28.1 - - + -
368A THR 4.0 0.2 - - - +
369A TYR* 3.6 5.1 - - - -
370A ALA* 2.9 33.4 + - - +
372A TRP* 3.8 11.4 - - + -
409A ASP* 1.3 82.1 - - - +
411A TRP* 1.3 84.7 + - - +
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Residues in contact with TRP 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 3.8 0.3 - - - +
15A GLY* 2.7 47.7 + - - -
367A ALA* 5.6 6.5 - - + -
368A THR 3.0 12.3 - - - +
369A TYR* 4.3 15.0 - + + -
410A GLU* 1.3 90.3 + - - +
412A THR* 1.3 72.9 + - - +
413A PHE* 3.4 40.8 - + + -
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Residues in contact with THR 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TRP 3.2 10.3 - - - -
14A THR* 3.8 18.2 - - - +
15A GLY 4.4 0.7 - - - +
20A GLN* 4.2 9.8 + - - -
21A GLN 3.5 25.0 + - - +
23A PHE* 3.6 17.3 - - + -
35A GLY 3.9 7.8 + - - -
366A PHE* 4.0 4.1 - - - -
367A ALA* 3.3 3.5 - - - +
368A THR* 2.6 55.9 + - - +
411A TRP* 1.3 82.8 - - - +
413A PHE* 1.3 63.0 + - - +
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Residues in contact with PHE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY* 3.3 2.6 - - - -
13A TRP* 2.8 74.6 + + + +
14A THR 4.9 0.7 - - - -
15A GLY* 4.6 8.7 - - - -
366A PHE* 3.2 22.4 - - - +
367A ALA* 4.2 7.4 - - + -
411A TRP* 3.4 37.7 - + + -
412A THR* 1.3 77.6 - - - +
414A GLY* 1.3 60.7 + - - +
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Residues in contact with GLY 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE 3.4 11.4 - - - -
13A TRP* 4.1 13.7 - - - -
365A VAL* 3.4 8.8 - - - +
366A PHE* 2.9 41.4 + - - +
413A PHE* 1.3 78.5 - - - +
415A ALA* 1.3 60.3 + - - -
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Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLY* 3.2 1.1 - - - -
11A ILE* 2.9 35.2 + - + +
13A TRP* 5.0 1.1 - - + -
363A ILE* 5.9 1.6 - - + -
364A ARG 3.1 11.4 - - - +
365A VAL* 4.3 12.1 - - + -
366A PHE* 3.8 2.6 - - - -
414A GLY* 1.3 74.5 - - - +
416A GLN* 1.3 65.2 + - - +
102C ALA* 4.5 5.2 - - + -
127C ALA* 3.6 30.1 - - + -
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Residues in contact with GLN 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 4.0 15.7 - - - +
9A SER 3.4 17.7 - - - +
10A GLY* 3.9 2.7 - - - +
35A GLY* 5.1 7.6 + - - -
37A GLU* 3.0 40.3 + - - +
39A GLU 5.7 1.0 + - - -
362A ALA 3.8 0.3 - - - +
363A ILE* 3.5 1.6 - - - +
364A ARG* 2.8 70.6 + - - +
366A PHE* 4.4 14.1 - - + -
415A ALA* 1.3 77.5 - - - +
417A MET* 1.3 73.7 + - - +
102C ALA* 4.0 8.2 - - - +
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Residues in contact with MET 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA* 3.9 18.8 - - + +
8A ARG* 3.4 2.1 - - - -
9A SER* 2.9 46.5 + - - +
362A ALA 3.2 10.8 - - - +
363A ILE* 4.5 6.3 - - + -
364A ARG* 5.1 0.2 - - - -
416A GLN* 1.3 84.1 - - - +
418A GLU* 1.3 69.5 + - - +
419A ILE* 4.0 3.4 - - - -
60C PHE* 4.1 17.3 - - + -
84C ALA* 3.6 31.2 - - + +
85C ASN* 3.9 5.2 - - - +
86C VAL* 3.8 26.9 - - + +
102C ALA* 3.4 24.7 - - + +
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TYR* 2.6 41.3 + - + +
7A ALA 3.4 5.8 - - - +
8A ARG* 4.5 2.9 - - + -
33A ARG* 3.3 19.3 + - - -
37A GLU* 4.4 2.9 - - - +
113A HIS* 3.7 8.1 + - - -
360A ARG* 2.8 27.6 + - - +
361A PRO* 3.2 3.5 - - - +
362A ALA 3.0 30.8 + - - +
364A ARG* 2.8 46.9 + - - +
417A MET* 1.3 76.5 - - - +
419A ILE* 1.3 65.8 + - - +
420A TRP* 4.1 1.6 - - + -
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TYR* 3.4 6.9 - - - -
7A ALA* 2.8 41.9 + - + +
360A ARG* 4.0 4.9 - - - -
361A PRO* 3.7 34.1 - - + -
417A MET* 4.0 8.7 - - - -
418A GLU* 1.3 78.4 - - - +
420A TRP* 1.3 78.7 + - - +
421A TRP* 4.0 12.8 - - + -
50C VAL* 4.0 13.7 - - + -
60C PHE* 3.6 53.2 - - + -
86C VAL* 4.3 2.2 - - + -
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Residues in contact with TRP 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLY 3.2 14.4 - - - +
6A TYR* 3.8 26.9 - + + -
113A HIS* 3.5 33.0 - + - -
358A TRP* 3.5 44.5 + + + +
360A ARG* 3.5 51.7 - - + +
361A PRO* 5.3 0.2 - - - +
418A GLU* 4.0 4.7 - - - -
419A ILE* 1.3 80.9 - - - +
421A TRP* 1.3 65.5 + - - +
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Residues in contact with TRP 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A PHE* 3.2 53.5 - + - +
4A HIS* 2.5 63.7 + - - +
5A GLY 2.9 33.2 + - - +
6A TYR 3.3 36.3 - - - -
7A ALA* 3.9 3.1 - - + -
43A GLU 3.6 9.4 - - - -
44A LEU* 4.1 4.9 - - + -
419A ILE* 4.0 12.3 - - + -
420A TRP* 1.3 82.2 - - - +
48C GLN* 4.1 13.4 + - + +
50C VAL* 4.3 23.3 - - + -
60C PHE* 3.3 42.2 - + - -
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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