Contacts of the strand formed by residues 408 - 421 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B LYS* 3.3 10.9 + - - +
372B TRP* 2.9 62.1 + - - +
405B ARG 4.9 1.6 - - - -
407B ASP* 1.3 80.3 + - - +
409B ASP* 1.3 70.9 + - - +
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Residues in contact with ASP 409 (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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369B TYR* 2.4 41.9 + - - -
370B ALA 3.5 4.2 - - - +
371B LYS* 3.0 20.5 - - - +
372B TRP* 3.8 6.3 - - - -
408B SER* 1.3 81.6 + - - +
410B GLU* 1.3 70.6 + - - +
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Residues in contact with GLU 410 (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 THR* 3.4 19.6 - - + +
15B GLY* 4.0 0.9 - - - -
16B SER* 2.4 45.5 + - - -
21B GLN* 4.8 7.2 + - - +
23B PHE* 3.8 27.7 - - + -
369B TYR* 3.6 5.1 - - - -
370B ALA* 2.9 33.1 + - - +
372B TRP* 3.9 11.2 - - + -
409B ASP* 1.3 82.5 - - - +
411B TRP* 1.3 85.7 + - - +
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Residues in contact with TRP 411 (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 THR* 3.7 0.5 - - - +
15B GLY* 2.7 53.3 + - - -
16B SER 4.7 0.2 - - - +
23B PHE* 5.2 0.4 - - - -
367B ALA* 5.5 6.5 - - + -
368B THR 3.0 12.1 - - - +
369B TYR* 4.3 13.9 - + + -
410B GLU* 1.3 91.9 + - - +
412B THR* 1.3 67.6 + - - +
413B PHE* 3.3 40.8 - + + -
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Residues in contact with THR 412 (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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13B TRP 3.2 13.5 - - - +
14B THR* 3.9 5.8 - - - +
15B GLY 4.4 0.7 - - - +
20B GLN* 4.2 9.7 + - - +
21B GLN 3.5 34.4 + - - +
23B PHE* 3.6 17.5 - - + -
35B GLY 3.9 8.5 + - - -
366B PHE* 4.0 2.8 - - - -
367B ALA* 3.3 3.5 - - - +
368B THR* 2.6 52.2 + - - +
411B TRP* 1.3 81.4 - - - +
413B PHE* 1.3 62.4 + - - +
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Residues in contact with PHE 413 (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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12B GLY* 3.3 2.8 - - - -
13B TRP* 2.8 77.3 + + + -
14B THR 4.9 0.4 - - - -
15B GLY* 4.6 8.1 - - - -
366B PHE* 3.2 25.0 - - - +
367B ALA* 4.2 7.6 - - + -
411B TRP* 3.3 38.4 - + + -
412B THR* 1.3 76.2 - - - +
414B GLY* 1.3 61.1 + - - +
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Residues in contact with GLY 414 (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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11B ILE 3.3 11.4 - - - -
12B GLY* 4.1 1.1 - - - -
13B TRP* 4.1 12.6 - - - -
365B VAL* 3.4 8.2 - - - +
366B PHE* 2.9 40.3 + - - +
413B PHE* 1.3 80.5 - - - +
415B ALA* 1.3 61.6 + - - -
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Residues in contact with ALA 415 (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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102A ALA* 4.5 5.2 - - + -
127A ALA* 3.6 30.3 - - + -
10B GLY* 3.3 1.4 - - - -
11B ILE* 2.9 36.0 + - + +
13B TRP* 5.1 1.1 - - + -
363B ILE* 5.9 1.6 - - + -
364B ARG 3.1 11.2 - - - +
365B VAL* 4.3 12.3 - - + -
366B PHE* 4.4 1.6 - - - -
414B GLY* 1.3 74.5 - - - +
416B GLN* 1.3 64.2 + - - +
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Residues in contact with GLN 416 (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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102A ALA* 4.0 7.7 - - - +
8B ARG* 4.0 16.0 - - - +
9B SER* 3.4 17.4 - - - +
10B GLY* 3.9 2.9 - - - +
35B GLY* 5.1 7.3 + - - -
37B GLU* 2.9 40.1 + - - +
39B GLU 5.7 0.6 + - - -
362B ALA 3.9 0.3 - - - +
363B ILE* 3.5 1.7 - - - +
364B ARG* 2.8 68.6 + - - +
366B PHE* 4.4 15.7 - - + -
415B ALA* 1.3 76.9 - - - +
417B MET* 1.3 73.7 + - - +
418B GLU* 5.0 0.4 - - - +
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Residues in contact with MET 417 (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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60A PHE* 4.1 8.1 - - + -
84A ALA* 3.6 30.5 - - + +
85A ASN* 3.9 4.9 - - - +
86A VAL* 3.8 28.5 - - + +
102A ALA* 3.4 25.2 - - + +
7B ALA* 3.9 27.6 - - + +
8B ARG* 3.4 2.3 - - - +
9B SER* 2.8 47.4 + - - +
362B ALA 3.2 10.5 - - - +
363B ILE* 4.5 6.5 - - + +
364B ARG* 5.2 0.4 - - - -
416B GLN* 1.3 83.5 - - - +
418B GLU* 1.3 68.1 + - - +
419B ILE* 4.0 3.4 - - - -
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Residues in contact with GLU 418 (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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6B TYR* 2.6 40.6 + - + +
7B ALA 3.4 6.5 - - - +
8B ARG* 4.6 3.3 - - + +
33B ARG* 3.3 19.1 + - - -
37B GLU* 4.4 3.7 - - - +
113B HIS* 3.6 7.8 + - - -
360B ARG* 2.8 36.2 + - - +
361B PRO* 3.3 3.1 - - - +
362B ALA 2.9 31.3 + - - +
364B ARG* 2.9 37.2 + - - +
417B MET* 1.3 76.6 - - - +
419B ILE* 1.3 65.3 + - - +
420B TRP* 4.1 1.3 - - + -
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Residues in contact with ILE 419 (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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50A VAL* 4.0 14.8 - - + -
60A PHE* 3.7 53.2 - - + -
86A VAL* 4.3 1.8 - - + -
6B TYR* 3.4 6.6 - - - -
7B ALA* 2.8 45.5 + - + +
360B ARG* 4.0 5.4 - - - -
361B PRO* 3.7 33.9 - - + -
417B MET* 4.0 7.0 - - - -
418B GLU* 1.3 78.8 - - - +
420B TRP* 1.3 77.6 + - - +
421B TRP* 4.0 9.2 - - + -
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Residues in contact with TRP 420 (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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5B GLY 3.2 13.2 - - - +
6B TYR* 3.9 26.2 - + + -
113B HIS* 3.5 31.2 - + - -
358B TRP* 3.5 45.2 + + - -
360B ARG* 3.5 54.1 - - + +
361B PRO* 5.3 0.2 - - - +
418B GLU* 3.9 4.5 - - - -
419B ILE* 1.3 80.7 - - - +
421B TRP* 1.3 65.0 + - - +
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Residues in contact with TRP 421 (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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48A GLN* 4.1 12.1 + - + +
50A VAL* 4.4 23.1 - - + -
60A PHE* 3.3 43.1 - + - -
3B PHE* 3.2 53.6 + + - +
4B HIS* 2.5 63.0 + - - +
5B GLY* 3.0 30.1 + - - +
6B TYR 3.3 37.0 - - - -
7B ALA 3.8 2.5 - - - -
43B GLU 3.6 9.9 - - - -
44B LEU* 4.1 5.2 - - + -
419B ILE* 4.0 12.3 - - + -
420B TRP* 1.3 82.6 - - - +
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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