Contacts of the strand formed by residues 397 - 406 (chain B) in PDB entry 3DGR
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 CYS 397 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A A12 4.5 1.0 + - - -
37B PHE* 3.5 20.2 - - + -
38B GLU 3.5 6.7 - - - -
39B CYS* 3.9 21.5 - - - +
40B ARG* 5.9 0.2 + - - -
153B VAL* 5.6 0.2 - - - -
156B TRP* 3.6 33.7 - - + -
159B ILE* 5.0 1.6 - - - -
160B THR* 4.1 8.5 - - - -
392B ARG* 3.0 41.1 + - + +
395B LEU* 3.9 14.8 - - - -
396B ASN* 1.3 73.9 - - - +
398B SER* 1.3 60.2 + - - +
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Residues in contact with SER 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A A12 2.5 25.7 + - - -
36B TYR 3.6 0.7 - - - +
37B PHE* 3.2 10.4 - - - -
38B GLU* 2.9 37.0 + - - +
40B ARG* 4.0 23.7 + - - -
153B VAL* 5.7 0.9 - - - -
392B ARG* 4.5 2.5 - - - +
396B ASN 3.7 9.6 - - - -
397B CYS* 1.3 77.2 - - - +
399B PHE* 1.3 59.8 + - - +
400B LYS* 3.1 18.2 + - - +
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Residues in contact with PHE 399 (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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501A A12 4.6 1.0 + - - -
35B SER* 3.5 28.9 - - - -
36B TYR 3.2 12.8 - - - -
37B PHE* 4.5 1.8 - - + -
132B PHE* 4.2 20.0 - + - -
134B VAL* 3.8 27.1 - - + -
145B THR 4.0 15.7 - - - -
146B ASN* 3.8 14.9 + - - -
149B GLU* 3.3 51.1 + - + +
152B LEU* 4.2 8.1 - - + -
153B VAL* 3.3 28.9 - - + +
392B ARG* 5.5 0.2 - - - +
398B SER* 1.3 74.8 + - - +
400B LYS* 1.3 81.4 + - - +
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A HIS* 4.7 13.0 + - + -
248A SER 6.1 0.9 - - - +
501A A12 2.5 44.6 + - - +
35B SER* 3.2 6.1 - - - -
36B TYR* 2.9 52.7 + - + +
40B ARG* 6.1 1.3 - - - +
146B ASN* 5.9 0.7 - - - +
149B GLU* 4.9 0.8 + - - -
398B SER* 3.1 15.2 + - - +
399B PHE* 1.3 87.4 + - - +
401B CYS* 1.3 65.1 + - - +
415B LYS* 3.6 39.3 - - + +
423B LYS 5.7 0.2 - - - -
425B SER* 4.1 19.3 - - - +
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Residues in contact with CYS 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A SER* 3.8 37.7 - - - +
251A THR* 4.6 4.6 + - - +
252A ALA* 5.2 3.8 - - - -
26B TYR* 5.8 0.2 - - - -
33B VAL* 3.8 17.0 - - + -
34B TYR 3.5 12.8 - - - -
35B SER* 3.1 14.9 + - - +
146B ASN* 5.1 1.0 + - - +
400B LYS* 1.3 79.1 - - - +
402B SER* 1.3 57.6 + - - +
403B TYR 3.7 11.0 - - - -
404B VAL* 4.8 5.2 - - - -
413B VAL* 3.6 32.4 - - + +
414B PHE* 4.3 5.2 + - - -
425B SER* 4.7 1.9 + - - -
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Residues in contact with SER 402 (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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34B TYR* 3.1 21.6 + - - -
36B TYR* 4.0 17.9 - - - -
400B LYS 3.5 1.6 + - - -
401B CYS* 1.3 72.3 - - - +
403B TYR* 1.3 56.8 + - - +
413B VAL* 3.0 25.5 + - - -
426B LYS 3.2 21.5 - - - -
428B GLY* 2.6 50.5 + - - -
430B LEU* 4.3 2.2 - - - +
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Residues in contact with TYR 403 (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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32B LYS* 4.6 9.0 - - + -
34B TYR* 2.9 57.2 + + + +
401B CYS* 3.7 3.5 - - - -
402B SER* 1.3 79.9 - - - +
404B VAL* 1.3 62.9 + - - +
405B VAL* 3.7 21.6 - - + +
410B GLY* 3.5 31.6 - - - -
411B ILE 3.5 16.6 - - - -
412B ASN* 3.7 17.5 - - - -
413B VAL* 3.5 2.3 - - - +
428B GLY 3.9 5.6 - - - -
429B ARG* 3.8 36.3 - - + -
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Residues in contact with VAL 404 (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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252A ALA* 3.4 39.3 - - + +
30B THR* 3.5 22.2 - - + +
32B LYS 3.0 20.0 - - - +
33B VAL* 4.1 11.0 - - + -
401B CYS* 4.8 3.6 - - - -
403B TYR* 1.3 76.8 - - - +
405B VAL* 1.3 58.9 + - - +
406B THR* 3.9 13.2 - - - +
409B LEU 3.8 0.2 - - - +
410B GLY* 3.3 2.1 - - - -
411B ILE* 2.7 44.6 + - + -
413B VAL* 4.1 13.5 - - + -
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Residues in contact with VAL 405 (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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30B THR* 3.3 6.6 - - - +
31B SER* 2.9 44.7 + - - +
32B LYS* 3.1 23.9 + - + -
403B TYR* 3.7 33.0 - - + +
404B VAL* 1.3 72.6 - - - +
406B THR* 1.3 61.5 + - - +
408B GLY* 3.6 32.8 - - - +
409B LEU 3.4 4.0 - - - +
410B GLY* 3.9 4.0 - - - +
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Residues in contact with THR 406 (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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252A ALA 4.7 0.5 + - - -
27B PRO* 3.9 20.8 - - + +
28B PRO 3.3 26.2 - - - +
29B ASN 3.3 5.2 - - - +
30B THR* 3.1 14.8 + - - +
404B VAL* 3.9 16.6 - - - +
405B VAL* 1.3 72.4 - - - +
407B ASN* 1.3 77.2 + - - +
408B GLY 3.2 1.1 - - - -
409B LEU* 2.9 31.5 + - - +
411B ILE* 5.3 4.7 - - - +
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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