Contacts of the strand formed by residues 92 - 98 (chain B) in PDB entry 5FHK
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 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ARG* 3.8 30.7 - - - +
91B GLY* 1.3 74.1 - - - +
93B ILE* 1.3 62.0 + - - +
94B LYS* 3.2 35.3 - - - +
121B ASN* 3.3 19.1 - - + +
123B GLU* 3.1 35.2 + - + +
139B ASP* 4.1 5.9 - - - +
277B LYS* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LYS* 1.3 78.8 - - - +
94B LYS* 1.3 56.3 + - - +
95B ILE* 3.6 22.6 + - + -
113B PHE* 4.2 5.4 - - + -
120B ILE* 3.8 25.4 - - + -
121B ASN 2.7 11.7 + - - +
122B ILE* 3.3 10.7 - - + +
123B GLU 2.8 31.7 + - - +
139B ASP* 3.6 17.0 - - + -
140B VAL* 5.1 0.9 - - + -
277B LYS* 3.3 40.4 - - + +
278B VAL* 4.4 4.9 - - + +
281B PHE* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LYS* 3.2 27.6 - - - +
93B ILE* 1.3 71.1 - - - +
95B ILE* 1.3 62.2 + - - +
123B GLU* 3.5 25.9 + - - +
125B THR* 5.3 0.2 - - - -
137B GLU* 3.9 33.2 + - - +
138B TRP* 3.5 40.2 - - + -
139B ASP* 2.8 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.6 24.7 - - + +
94B LYS* 1.3 81.2 - - - +
96B SER* 1.3 61.7 + - - +
97B THR* 4.3 7.9 - - + -
110B LEU* 3.8 36.6 - - + -
122B ILE* 4.0 16.4 - - + -
123B GLU 2.9 15.6 + - - +
124B LEU* 4.1 13.0 - - + -
125B THR 3.1 22.5 + - - -
138B TRP* 3.6 9.5 - - - -
140B VAL* 3.3 16.8 - - + +
142B PHE* 4.4 5.8 - - + -
281B PHE* 4.2 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 1.3 75.0 - - - +
97B THR* 1.3 64.9 + - - +
125B THR 3.4 8.3 - - - -
127B GLU* 3.5 15.9 - - - +
130B ALA* 5.2 0.5 - - - +
133B LEU* 3.4 31.5 - - - +
138B TRP* 3.9 19.7 - - - -
140B VAL 3.2 5.1 + - - -
141B ILE* 4.3 8.1 - - - +
142B PHE* 2.7 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 4.3 7.2 - - + -
96B SER* 1.3 83.7 + - - +
98B PRO* 1.3 70.8 - - - +
102B THR* 2.6 31.5 + - - +
106B MET* 4.0 14.6 - - + -
110B LEU* 4.7 0.2 - - + -
124B LEU* 3.8 26.0 - - + +
125B THR 3.1 3.8 + - - -
126B THR* 3.5 8.8 - - - +
127B GLU* 2.9 27.8 + - - +
142B PHE* 3.6 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B THR* 1.3 86.0 - - - +
99B TYR* 1.3 63.0 + - - +
100B ASN 3.4 1.1 - - - -
101B LEU* 3.9 32.3 - - + -
102B THR* 2.4 32.3 + - - +
105B MET* 6.3 0.4 - - - -
106B MET* 4.4 10.3 - - + -
127B GLU 3.8 4.7 - - - +
142B PHE* 3.3 30.0 - - + +
143B ARG* 4.1 12.6 - - - +
144B VAL* 4.7 9.9 - - + +
264B ILE* 5.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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