Contacts of the strand formed by residues 441 - 447 (chain C) in PDB entry 3GEB
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 441 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269C ARG* 3.4 10.8 - - - -
271C PHE* 3.7 27.8 - - + -
435C ILE* 3.0 33.8 - - + +
436C ASN* 4.4 3.6 - - - +
438C ARG* 3.4 52.6 - - + +
439C PRO 3.3 4.5 + - - +
440C ASN* 1.3 83.7 - - - +
442C VAL* 1.3 67.1 + - - +
533C LEU* 5.0 0.9 - - - -
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Residues in contact with VAL 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C GLU* 6.0 2.2 - - - +
269C ARG 2.9 13.5 + - - +
270C VAL* 4.5 6.3 - - + -
271C PHE* 2.8 35.7 + - - +
435C ILE* 3.7 4.7 - - - -
440C ASN 5.4 1.8 - - - -
441C CYS* 1.3 82.4 - - - +
443C ASN* 1.3 63.5 + - - +
444C VAL* 4.0 8.1 - - + -
468C PRO* 6.1 0.2 - - + -
471C ASN* 3.4 26.0 - - - +
491C PHE* 4.0 22.2 - - + -
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Residues in contact with ASN 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C PHE 3.9 1.1 - - - -
273C TRP* 2.8 27.5 + - - -
432C LEU* 3.0 37.7 + - - +
435C ILE* 3.1 23.2 - - - +
436C ASN* 3.4 21.4 - - - +
442C VAL* 1.3 72.5 - - - +
444C VAL* 1.3 55.6 + - - +
466C VAL* 3.9 8.5 + - - +
467C PHE* 3.4 22.1 - - + -
468C PRO* 4.3 3.8 - - + +
471C ASN* 2.6 31.4 + - - +
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Residues in contact with VAL 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C VAL* 3.4 29.6 - - + -
271C PHE 2.8 15.0 + - - +
272C VAL* 4.3 3.6 - - + -
273C TRP* 2.8 29.9 + - - -
442C VAL* 4.0 1.3 - - + -
443C ASN* 1.3 74.1 - - - +
445C LEU* 1.3 66.9 + - - +
467C PHE* 3.9 1.1 - - - -
471C ASN* 3.5 31.4 - - - +
473C TYR* 4.0 8.1 - - + -
487C ILE* 3.5 33.9 - - + -
491C PHE* 3.6 16.6 - - + -
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Residues in contact with LEU 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C TRP* 3.4 27.6 - - + +
274C ASP 4.0 14.1 - - - +
275C LEU* 4.1 19.1 - - + +
279C ILE* 4.5 1.8 - - + -
444C VAL* 1.3 76.6 - - - +
446C VAL* 1.3 72.5 + - - +
447C THR* 4.5 4.9 - - + +
454C ALA* 6.0 0.2 - - + -
458C VAL* 4.0 23.8 - - + -
467C PHE* 3.9 29.3 - - + -
471C ASN 3.1 10.2 + - - +
472C ILE* 3.7 27.1 - - + -
473C TYR* 2.9 26.3 + - - +
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Residues in contact with VAL 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C VAL* 3.6 11.4 - - + -
273C TRP 2.8 20.3 + - - +
274C ASP* 3.9 8.1 - - - +
445C LEU* 1.3 81.4 - - - +
447C THR* 1.3 59.7 + - - +
473C TYR* 3.4 11.2 - - + +
475C ALA* 4.2 5.4 - - + -
480C LYS* 3.7 38.1 - - + +
483C CYS* 4.0 16.8 - - + -
484C PHE* 3.9 18.4 - - + -
487C ILE* 3.4 31.9 - - + -
506C GLU* 5.7 0.2 - - - +
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Residues in contact with THR 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C ASP* 5.1 2.7 - - - -
275C LEU* 4.3 25.8 - - - +
276C ASP* 5.7 0.3 + - - -
445C LEU* 4.8 4.7 - - + -
446C VAL* 1.3 74.6 - - - +
448C THR* 1.3 66.7 + - - +
449C THR* 3.0 27.8 + - - +
454C ALA* 3.8 26.2 - - + -
472C ILE* 4.8 10.3 - - + -
473C TYR 3.0 12.0 + - - +
474C SER* 3.5 3.3 - - - -
475C ALA* 2.7 36.8 + - - +
480C LYS* 4.4 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