Contacts of the strand formed by residues 397 - 406 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.6 12.3 - - + -
38A GLU 3.5 7.0 - - - -
39A CYS* 3.8 22.7 - - - +
40A ARG* 5.2 0.2 + - - -
156A TRP* 3.6 39.7 - - + -
159A ILE* 5.0 1.8 - - - -
160A THR* 4.1 13.0 - - - -
392A ARG* 3.1 40.9 + - + +
395A LEU* 4.2 9.0 - - - -
396A ASN* 1.3 75.1 - - - +
398A SER* 1.3 59.2 + - - +
501B A12 4.4 1.4 - - - +
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Residues in contact with SER 398 (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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36A TYR* 3.7 1.6 - - - +
37A PHE* 3.3 10.0 - - - -
38A GLU* 2.9 37.1 + - - +
40A ARG* 3.4 32.6 + - - -
153A VAL* 5.6 0.9 - - - -
392A ARG* 4.2 2.5 - - - +
396A ASN 3.7 3.6 - - - -
397A CYS* 1.3 74.8 - - - +
399A PHE* 1.3 57.8 + - - +
400A LYS* 3.1 18.2 + - - +
501B A12 2.5 23.6 + - - -
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Residues in contact with PHE 399 (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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35A SER* 3.5 27.8 - - - -
36A TYR 3.2 14.8 - - - -
37A PHE* 4.4 4.5 - + + -
132A PHE* 4.1 18.6 - + - -
134A VAL* 3.8 27.4 - - + -
145A THR 3.9 14.8 - - - -
146A ASN* 3.6 17.1 + - - -
149A GLU* 3.3 47.5 + - + +
152A LEU* 4.4 7.6 - - + -
153A VAL* 3.4 29.2 - - + +
392A ARG* 5.1 1.0 - - - +
398A SER* 1.3 73.9 + - - +
400A LYS* 1.3 83.1 + - - +
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Residues in contact with LYS 400 (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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35A SER* 3.8 5.4 - - - -
36A TYR* 2.9 43.7 + - + +
40A ARG* 5.8 0.2 - - - +
146A ASN* 5.6 1.3 - - - +
149A GLU* 4.5 1.0 + - - -
398A SER* 3.1 13.4 + - - +
399A PHE* 1.3 92.6 + - - +
401A CYS* 1.3 65.8 + - - +
415A LYS* 3.8 34.8 - - + +
425A SER* 4.1 26.0 - - - +
247B HIS* 4.6 14.1 - - + -
248B SER 6.0 0.7 - - - +
501B A12 2.7 47.5 + - - +
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Residues in contact with CYS 401 (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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26A TYR* 5.7 0.2 - - - -
33A VAL* 4.0 16.6 - - + -
34A TYR 3.6 9.6 - - - -
35A SER* 3.3 15.5 + - - +
36A TYR* 5.3 0.2 - - - -
146A ASN* 5.0 0.6 - - - +
400A LYS* 1.3 79.7 - - - +
402A SER* 1.3 58.4 + - - +
403A TYR 3.8 12.1 - - - -
404A VAL* 4.9 5.2 - - - -
413A VAL* 3.4 35.6 - - + +
414A PHE* 4.4 4.3 + - - -
425A SER* 4.7 2.3 + - - -
426A LYS 4.7 0.2 - - - +
248B SER* 3.7 37.0 - - - +
251B THR* 4.7 3.5 + - - +
252B ALA* 5.0 4.5 - - - -
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Residues in contact with SER 402 (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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34A TYR* 3.0 23.9 + - - -
36A TYR* 3.9 19.3 - - - -
400A LYS 3.6 1.6 + - - -
401A CYS* 1.3 72.4 - - - +
403A TYR* 1.3 59.3 + - - +
413A VAL* 2.9 24.6 + - - -
426A LYS 3.3 22.0 - - - -
428A GLY* 2.7 46.9 + - - -
430A LEU* 4.1 2.5 - - - +
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Residues in contact with TYR 403 (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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32A LYS* 4.4 10.8 - - + -
33A VAL* 3.7 1.0 - - - -
34A TYR* 2.8 62.8 + + + +
401A CYS* 3.8 4.3 - - - -
402A SER* 1.3 80.6 - - - +
404A VAL* 1.3 59.2 + - - +
405A VAL* 3.8 21.3 - - + +
410A GLY* 3.6 33.4 - - - -
411A ILE 3.5 15.0 - - - -
412A ASN* 3.8 16.8 - - - -
413A VAL* 3.6 3.7 - - - +
428A GLY 3.9 4.9 - - - -
429A ARG* 3.7 39.5 - - + -
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Residues in contact with VAL 404 (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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30A THR* 3.2 25.4 - - + +
32A LYS 2.9 21.3 - - - +
33A VAL* 4.4 6.3 - - + -
401A CYS* 5.0 3.1 - - - -
403A TYR* 1.3 77.3 - - - +
405A VAL* 1.3 66.6 + - - +
406A THR* 3.7 13.9 - - - +
409A LEU 3.8 0.2 - - - +
410A GLY* 3.4 3.5 - - - -
411A ILE* 2.9 55.4 + - + -
413A VAL* 4.0 7.2 - - + +
252B ALA* 3.6 28.7 - - + +
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Residues in contact with VAL 405 (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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30A THR* 3.1 5.7 - - - +
31A SER* 2.7 47.8 + - - +
32A LYS* 3.0 29.3 + - + -
403A TYR* 3.8 29.6 - - + +
404A VAL* 1.3 77.4 - - - +
406A THR* 1.3 59.8 + - - +
408A GLY* 3.8 31.0 - - - +
409A LEU 3.4 2.7 - - - +
410A GLY* 4.0 4.3 - - - +
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Residues in contact with THR 406 (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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27A PRO* 4.2 13.8 - - + +
28A PRO 3.5 23.3 - - - +
29A ASN 3.2 3.8 - - - +
30A THR* 2.8 19.2 + - - +
404A VAL* 3.7 15.7 - - - +
405A VAL* 1.3 73.7 - - - +
407A ASN* 1.3 83.7 + - + +
408A GLY 3.2 0.9 - - - -
409A LEU* 3.0 23.3 + - - +
411A ILE* 6.0 4.7 - - - -
252B ALA 4.8 0.9 + - - -
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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