Contacts of the strand formed by residues 77 - 83 (chain D) in PDB entry 5FFO
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 LYS 77 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C GLU* 3.3 3.5 - - - -
349C GLN* 3.0 35.5 + - + +
351C SER* 6.4 1.1 - - - -
72D ALA* 2.6 37.6 + - - +
73D ASP* 4.4 13.4 - - - +
75D TYR* 3.9 14.5 + - - +
76D ALA* 1.3 84.1 + - - +
78D GLU* 1.3 64.4 + - - +
79D VAL* 3.3 7.7 + - + +
120D LEU 6.0 0.9 - - - +
122D SER* 4.1 32.2 + - - +
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Residues in contact with GLU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C PRO 5.5 0.7 - - - +
346C LYS* 3.9 40.3 + - + +
347C VAL 4.1 7.4 - - - +
348C GLU* 3.6 23.4 - - + +
76D ALA 4.3 0.6 + - - -
77D LYS* 1.3 70.9 - - - +
79D VAL* 1.3 62.1 + - - +
80D THR* 3.6 25.9 + - + +
114D ALA 5.7 2.8 - - - +
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Residues in contact with VAL 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C PRO* 6.2 0.4 - - + -
347C VAL* 2.7 31.8 + - + +
348C GLU 4.5 0.7 - - - -
349C GLN* 3.8 32.5 - - + +
51D LEU* 3.8 24.6 - - + +
55D THR* 3.7 27.4 - - + -
77D LYS* 3.3 16.4 + - + +
78D GLU* 1.3 70.3 - - - +
80D THR* 1.3 70.8 + - - +
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Residues in contact with THR 80 (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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347C VAL 6.2 0.4 - - - +
51D LEU* 3.6 13.0 - - + -
78D GLU* 3.6 28.6 + - + +
79D VAL* 1.3 82.4 - - - +
81D ARG* 1.3 62.8 + - - +
114D ALA* 3.6 36.0 + - + +
115D VAL* 4.9 5.4 - - - +
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Residues in contact with ARG 81 (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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47D ALA* 5.0 4.6 + - - +
50D ALA* 3.3 41.4 + - - +
51D LEU* 3.4 30.6 - - + +
54D SER* 4.7 14.0 + - - +
80D THR* 1.3 78.8 - - - +
82D VAL* 1.3 74.8 + - - +
83D LEU* 4.2 33.7 - - + +
114D ALA* 5.5 0.3 - - - +
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Residues in contact with VAL 82 (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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81D ARG* 1.3 82.7 - - - +
83D LEU* 1.3 70.0 + - - +
106D PHE* 3.6 16.1 - - + -
110D GLU* 4.0 40.4 - - + +
111D LEU* 3.6 34.3 - - + -
114D ALA* 4.8 9.4 - - + -
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Residues in contact with LEU 83 (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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81D ARG* 4.2 37.7 - - - +
82D VAL* 1.3 81.4 - - - +
84D MET* 1.3 68.2 + - - +
85D VAL* 5.6 0.2 - - - +
106D PHE* 3.5 10.0 - - - +
107D GLN 5.6 1.0 + - - -
110D GLU* 5.3 4.8 + - - +
111D LEU* 5.9 0.2 - - - +
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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