Contacts of the strand formed by residues 401 - 408 (chain A) in PDB entry 4IF8
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 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ALA* 3.7 10.7 - - - +
52A ASN* 2.8 24.8 + - - -
77A LEU* 3.5 15.7 - - - +
119A ILE* 4.4 5.4 - - - +
123A LEU* 5.0 2.9 - - - -
395A TYR* 3.4 15.1 - - - -
396A SER* 2.8 36.8 + - - -
399A ILE 3.4 4.2 + - - -
400A PRO* 1.4 75.9 + - - +
402A VAL* 1.3 58.0 + - - +
403A LEU* 3.5 20.5 + - - -
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Residues in contact with VAL 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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49A ALA 5.1 0.2 - - - +
52A ASN* 3.0 12.3 + - - +
53A MET* 3.9 38.6 - - + -
57A PHE* 6.0 1.1 - - + -
76A PRO* 3.8 18.5 - - + +
77A LEU* 3.4 25.1 + - - +
393A LEU* 4.6 16.4 - - + -
394A ILE 3.7 5.6 - - - +
395A TYR* 4.0 16.8 - - + -
401A SER* 1.3 70.3 - - - +
403A LEU* 1.3 62.2 + - - +
404A PHE 3.5 27.1 - - - +
405A LEU* 4.3 7.6 - - + -
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Residues in contact with LEU 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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75A SER* 2.5 32.2 + - - -
77A LEU* 3.7 13.9 - - + -
123A LEU* 3.5 29.6 - - + -
132A LEU* 3.8 24.9 - - + -
208A ILE* 4.2 5.5 - - + +
210A PHE* 4.3 2.9 - - + -
268A ILE* 4.0 32.1 - - + -
394A ILE* 2.8 16.8 + - + +
396A SER* 3.9 22.7 - - - +
401A SER* 4.0 4.7 - - - -
402A VAL* 1.3 73.0 - - - +
404A PHE* 1.3 78.9 + - + +
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Residues in contact with PHE 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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73A PHE* 3.4 33.9 - + + -
74A LEU 3.5 6.7 - - - -
75A SER* 4.3 0.7 - - - -
76A PRO* 4.3 0.7 - - - -
132A LEU* 5.6 0.2 - - + -
208A ILE* 3.8 39.5 - - + -
209A PHE 4.3 0.4 - - - -
210A PHE* 3.4 39.5 - + + -
356A ALA* 3.9 14.1 - - + -
357A GLU 3.7 17.3 - - - -
358A LEU* 3.9 10.1 - - + -
392A LEU 4.4 1.1 - - - +
393A LEU* 3.4 3.5 - - - -
394A ILE* 2.8 43.9 + - + -
402A VAL* 3.5 8.9 - - - +
403A LEU* 1.3 94.7 - - + +
405A LEU* 1.3 61.0 + - - +
406A GLY 4.3 0.2 - - - -
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Residues in contact with LEU 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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56A GLY* 3.2 40.8 - - - +
57A PHE* 3.9 15.3 - - + +
60A LEU* 3.9 30.5 - - + -
72A ILE* 3.9 2.1 - - - +
73A PHE* 3.7 4.1 - - - -
74A LEU* 2.9 38.4 + - + +
76A PRO* 4.1 13.9 - - + +
391A LEU* 5.3 2.7 - - + -
392A LEU 3.5 2.2 - - - +
393A LEU* 3.8 31.4 - - + -
402A VAL* 4.3 4.5 - - + -
404A PHE* 1.3 75.0 - - - +
406A GLY* 1.3 66.5 + - - +
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Residues in contact with GLY 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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60A LEU* 5.4 1.8 - - - -
72A ILE 3.1 9.6 - - - -
73A PHE* 3.9 14.7 - - - -
391A LEU* 3.2 8.7 - - - +
392A LEU* 2.8 42.8 + - - +
405A LEU* 1.3 79.1 - - - +
407A LYS* 1.3 60.0 + - - -
408A ILE* 3.9 7.2 - - - -
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Residues in contact with LYS 407 (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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60A LEU* 3.9 14.1 - - + +
64A ALA* 3.8 13.5 + - + +
67A ASN 4.9 0.4 + - - -
68A PRO* 4.4 5.7 - - - +
69A GLY 4.3 15.2 - - - +
70A ARG 3.8 13.3 + - - +
71A ASN* 3.3 7.3 - - - -
72A ILE* 2.7 47.8 + - + +
280A LEU* 3.8 17.9 - - + +
284A GLU* 2.7 30.4 + - - +
389A PRO* 6.2 0.4 - - + -
390A TYR 3.7 5.4 - - - +
391A LEU* 3.7 20.0 - - + -
406A GLY* 1.3 70.2 - - - -
408A ILE* 1.3 64.6 + - - +
409A VAL* 3.5 26.2 - - + -
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Residues in contact with ILE 408 (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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71A ASN* 3.5 3.1 - - - +
72A ILE 4.7 0.2 - - - +
73A PHE* 4.4 3.4 - - + -
228A PHE* 4.2 0.7 - - - -
311A LEU* 4.1 7.6 - - + -
313A MET* 3.8 33.7 - - + -
389A PRO* 3.2 4.2 - - - +
390A TYR* 2.8 79.5 + - + +
392A LEU* 4.5 10.3 - - + -
406A GLY* 4.2 10.1 - - - -
407A LYS* 1.3 83.0 - - - +
409A VAL* 1.3 59.8 + - - +
410A ASN 3.8 4.3 - - - +
411A PRO* 3.6 34.8 - - + -
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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