Contacts of the strand formed by residues 120 - 129 (chain E) in PDB entry 5FWP
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 120 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B VAL* 3.5 21.7 - - - +
324B GLU 3.0 8.5 - - - -
325B GLY* 4.4 0.2 - - - -
327B LEU* 3.1 29.4 - - - +
403B VAL* 5.5 0.3 - - - +
407B ASN* 3.8 16.1 + - - -
115E ASN 4.4 1.4 + - - -
116E VAL 3.4 18.8 + - - +
117E ASP* 4.6 1.6 - - - -
118E THR 3.4 1.2 - - - -
119E LEU* 1.3 84.6 - - - +
121E LYS* 1.3 73.8 + - - +
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Residues in contact with LYS 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B VAL* 3.1 9.6 - - - +
324B GLU* 2.8 28.9 + - + +
117E ASP* 3.0 29.8 + - - +
118E THR* 5.6 2.0 - - - +
120E SER* 1.3 82.0 - - - +
122E ASP* 1.3 61.7 + - - +
123E GLY* 2.8 10.6 + - - -
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Residues in contact with ASP 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B PHE* 3.7 8.7 - - + -
322B SER 3.7 4.3 - - - +
323B VAL* 5.0 0.2 - - - -
411B LYS* 2.8 33.7 + - - -
121E LYS* 1.3 71.6 - - - +
123E GLY* 1.3 61.8 + - - +
124E PHE* 3.3 24.5 - - - +
125E SER* 3.7 7.3 - - - -
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Residues in contact with GLY 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B SER* 2.8 17.4 + - - -
324B GLU* 3.8 36.9 - - - +
121E LYS* 2.8 8.0 + - - -
122E ASP* 1.3 72.5 - - - +
124E PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ASN* 4.7 2.7 - - - -
293B PRO* 3.4 42.0 - - + -
294B ASP* 4.0 26.7 - - - -
320B HIS* 3.3 19.7 - + + +
321B PHE* 3.3 5.7 - - - -
322B SER* 2.8 43.1 + - - -
122E ASP* 3.3 8.4 - - - +
123E GLY* 1.3 82.8 - - - +
125E SER* 1.3 77.3 + - - +
126E LYS* 3.4 20.0 - - + -
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Residues in contact with SER 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B LYS* 3.5 17.7 + - - -
320B HIS 3.4 5.4 - - - -
321B PHE* 4.8 0.2 - - - -
411B LYS* 3.1 33.2 + - - -
414B GLU* 4.3 0.7 + - - -
122E ASP* 3.7 8.3 - - - -
124E PHE* 1.3 83.9 - - - +
126E LYS* 1.3 64.6 + - - +
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Residues in contact with LYS 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B PRO* 3.4 36.1 - - + +
294B ASP* 2.8 32.1 + - - +
296B ILE 5.3 0.4 - - - -
301B TYR* 4.3 5.3 + - + +
318B VAL 3.9 0.5 - - - +
319B LYS* 3.2 6.1 - - - -
320B HIS* 2.8 39.8 + - + +
124E PHE* 3.4 14.6 - - + -
125E SER* 1.3 77.3 + - - +
127E SER* 1.3 68.2 + - - +
128E MET* 4.6 19.9 - - + +
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Residues in contact with SER 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B VAL 3.4 5.6 - - - -
319B LYS* 3.8 16.2 - - - +
415B LEU* 3.9 14.8 - - - -
418B GLU* 2.6 33.3 + - - -
126E LYS* 1.3 85.0 - - - +
128E MET* 1.3 68.3 + - - +
129E VAL* 6.2 0.4 - - - -
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Residues in contact with MET 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B ILE 4.3 8.3 - - - +
297B THR* 5.4 0.2 - - - -
298B GLN* 3.1 39.7 - - + +
301B TYR* 3.7 35.9 - - + -
317B ALA* 3.2 4.0 - - - +
318B VAL* 2.8 48.0 + - + +
415B LEU* 4.4 0.8 - - - +
126E LYS* 4.6 15.7 - - + +
127E SER* 1.3 82.6 - - - +
129E VAL* 1.3 69.0 + - - +
130E ASN 3.9 0.2 + - - -
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B GLN* 4.7 0.2 - - - +
316B LEU 3.6 10.3 - - - +
317B ALA* 4.2 6.5 - - + -
415B LEU* 4.8 6.1 - - + -
418B GLU* 4.7 7.6 - - + +
419B LEU* 3.7 46.2 - - + +
422B ASP* 3.7 10.8 - - + +
425B ASN* 4.1 5.8 - - + +
127E SER* 6.2 0.2 - - - -
128E MET* 1.3 84.0 - - - +
130E ASN* 1.3 60.5 + - - +
131E THR* 2.8 32.2 + - - +
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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