Contacts of the strand formed by residues 28 - 32 (chain D) in PDB entry 1FBA
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 GLY 28 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D ILE 4.5 2.7 - - - -
27D LYS* 1.3 75.4 - - - +
29D ILE* 1.3 64.9 + - - -
72D ASN 2.9 7.5 + - - -
73D ILE* 3.3 8.8 - - - -
74D SER* 2.9 27.5 + - - -
75D GLY 3.9 0.2 + - - -
298D THR* 3.6 5.8 - - - -
299D PHE* 3.4 28.1 - - - -
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Residues in contact with ILE 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.6 33.2 - - + -
28D GLY* 1.3 75.6 - - - -
30D LEU* 1.3 66.3 - - - +
73D ILE* 4.6 0.2 - - - -
74D SER* 4.5 2.0 - - - +
75D GLY 3.5 15.0 - - - +
77D ILE* 3.5 29.8 - - + -
144D PHE* 4.4 7.2 - - + -
185D ILE* 3.7 28.0 - - + -
268D THR* 3.9 20.4 - - + +
299D PHE* 2.8 19.4 + - - +
300D SER* 3.4 16.9 - - - +
301D TYR 3.0 25.3 + - - +
305D LEU* 3.8 0.3 - - - +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D GLY 4.2 0.6 + - - -
29D ILE* 1.3 74.5 - - - +
31D ALA* 1.3 63.1 + - - +
32D ALA* 3.4 6.4 + - + -
62D LEU* 4.9 15.0 - - + +
63D PHE* 4.9 6.1 - - + -
69D LEU* 5.3 6.1 - - + -
73D ILE* 4.0 20.4 - - + +
75D GLY 3.1 5.3 + - - +
76D VAL* 3.2 22.7 - - + +
77D ILE 3.0 21.5 + - - -
301D TYR 3.5 7.2 - - - +
305D LEU* 3.7 31.4 - - + -
306D GLN* 4.1 22.7 - - + +
327D LEU* 4.6 24.0 - - + -
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ILE 3.9 1.6 - - - -
30D LEU* 1.3 68.9 - - - +
32D ALA* 1.3 59.0 + - - +
33D ASP* 3.4 17.6 + - - +
34D GLU* 3.9 3.1 - - - +
77D ILE* 4.1 23.3 - - + -
146D LYS* 5.7 0.7 - - - +
229D LYS* 4.3 13.0 - - - +
300D SER* 4.5 1.6 - - - +
301D TYR 2.9 20.1 + - - +
302D GLY* 3.4 14.1 - - - +
306D GLN* 3.1 19.7 + - - -
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Residues in contact with ALA 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.4 7.2 + - + +
31D ALA* 1.3 72.5 - - - +
33D ASP* 1.3 57.0 + - - +
34D GLU* 3.2 19.9 + - - +
59D ARG* 3.4 16.6 + - - +
62D LEU* 4.6 15.3 - - + -
63D PHE* 4.4 18.3 - - + -
76D VAL* 4.1 16.2 - - + -
77D ILE 2.8 16.8 + - - +
78D LEU* 4.3 3.0 - - + +
79D PHE 4.2 5.5 + - - -
82D THR* 5.0 1.4 + - - +
306D GLN* 4.3 2.0 - - - +
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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