Contacts of the strand formed by residues 79 - 90 (chain B) in PDB entry 5FJV
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 MET 79 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 4.1 21.5 - - + -
71B ASP 3.4 8.5 - - - +
72B VAL* 4.2 8.5 - - + +
78B MET* 1.3 77.3 - - - +
80B THR* 1.3 68.2 + - - +
81B THR* 4.2 8.5 + - + +
153B TYR 3.7 0.9 - - - +
154B LYS* 3.3 2.3 - - - -
155B SER* 2.7 63.6 + - - +
156B SER* 4.0 0.4 - - - +
157B CYS* 4.1 1.8 - - + -
171B CYS* 3.1 52.7 - - + +
172B LYS 4.7 1.3 - - - +
173B MET* 4.6 12.1 - - + +
233B PHE* 5.4 9.2 - - - -
235B ILE* 5.1 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ASP* 6.2 0.4 - - + -
69B LEU* 3.4 8.1 - - - +
70B ILE* 2.9 51.2 + - + -
71B ASP* 2.5 31.3 + - - +
78B MET* 5.1 5.4 - - - +
79B MET* 1.3 73.1 - - - +
81B THR* 1.3 67.6 + - - +
152B ILE* 4.5 11.0 - - + -
153B TYR 3.2 7.0 - - - +
154B LYS* 3.3 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 5.0 10.1 - - + -
68B GLN 3.8 4.9 - - - +
69B LEU* 3.3 27.8 - - + -
70B ILE* 4.4 4.9 - - - -
79B MET* 4.5 11.3 + - + +
80B THR* 1.3 71.9 - - - +
82B ASN* 1.3 60.1 + - - +
83B VAL* 3.9 17.2 + - + -
151B ALA 3.5 0.5 - - - +
152B ILE* 3.3 7.6 - - - +
153B TYR* 2.7 50.8 + - - +
155B SER* 4.5 4.0 + - - -
173B MET* 3.9 17.2 - - - +
207B ILE* 5.7 1.6 - - + -
233B PHE* 5.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR 4.3 2.2 + - - -
124A ASN* 3.1 27.3 + - + +
129A PHE* 3.1 20.3 - - - -
66B ILE* 4.0 1.6 - - - +
67B ALA* 3.0 52.6 + - - +
68B GLN* 2.7 26.8 + - + +
70B ILE* 4.3 3.8 - - + +
81B THR* 1.3 72.4 - - - +
83B VAL* 1.3 65.7 + - - +
84B TRP* 4.4 4.6 + - - +
151B ALA 3.2 3.9 - - - +
152B ILE* 3.0 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.5 25.4 - - + -
65B SER 3.7 4.0 - - - +
66B ILE* 3.9 19.1 - - + -
81B THR* 3.9 22.9 - - + +
82B ASN* 1.3 79.4 - - - +
84B TRP* 1.3 70.8 + - - +
85B LEU* 4.9 1.3 - - + +
150B PRO 3.2 1.2 - - - -
151B ALA* 2.5 52.4 + - + -
153B TYR* 3.3 35.7 - - + -
173B MET* 4.7 4.0 - - + -
175B PHE* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 4.0 18.3 + + - -
129A PHE* 5.9 0.4 - - - -
178A TRP* 3.2 37.2 - + - -
219A TYR* 4.4 5.8 - + + -
221A CYS* 5.2 7.6 - - - -
300A EPJ 3.6 31.2 - - + -
63B GLY 3.4 1.9 - - - +
64B LEU* 3.5 6.3 - - - +
65B SER* 3.2 47.5 + - - +
67B ALA* 3.6 29.3 - - + +
82B ASN* 4.4 5.2 + - - +
83B VAL* 1.3 87.5 - - - +
85B LEU* 1.3 61.8 + - - +
86B LYS* 3.3 5.9 + - + +
148B VAL* 3.8 21.8 - - + -
149B PRO 3.3 5.6 - - - +
150B PRO* 4.2 3.3 - - + +
199B TYR* 4.3 33.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 3.1 38.8 - - + -
63B GLY 4.5 1.6 - - - +
64B LEU* 3.7 24.0 - - + -
83B VAL* 4.1 2.1 - - + +
84B TRP* 1.3 70.6 - - - +
86B LYS* 1.3 63.6 + - - +
87B GLN* 3.3 14.1 + - - +
119B ILE* 4.4 12.1 - - + +
131B VAL* 4.1 14.8 - - + -
147B TRP 3.2 13.0 - - - +
148B VAL* 3.4 2.0 - - - -
149B PRO* 3.0 26.9 + - + +
151B ALA* 5.5 1.1 - - + +
153B TYR* 3.9 25.6 - - + +
175B PHE* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A CYS* 3.8 21.3 - - + -
61B ARG 3.7 0.6 - - - +
62B PHE* 3.5 2.1 - - - -
63B GLY* 2.5 61.4 + - - +
64B LEU 3.6 10.1 + - - +
65B SER* 3.2 28.0 + - - +
84B TRP* 4.1 5.4 - - + +
85B LEU* 1.3 71.7 - - - +
87B GLN* 1.3 64.1 + - - +
148B VAL* 3.6 29.8 - - + -
190B MET* 3.9 20.5 - - + +
191B GLU 5.1 0.4 + - - -
192B GLN* 5.7 1.6 + - - -
194B VAL* 3.2 38.2 + - - +
195B ASP 3.8 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 4.2 5.8 - - + +
61B ARG 3.3 3.4 - - - -
62B PHE* 3.8 18.8 - - + -
85B LEU* 3.5 27.8 - - - +
86B LYS* 1.3 80.0 - - - +
88B GLU* 1.3 63.6 + - - +
89B TRP* 3.8 12.5 - - + -
117B PRO* 3.7 38.0 + - - +
119B ILE* 4.2 10.7 - - - +
131B VAL* 4.9 0.7 - - - +
146B HIS* 3.6 2.8 - - - +
147B TRP* 2.8 65.1 + - - +
148B VAL* 4.1 2.2 - - - +
149B PRO* 4.0 2.9 - - - +
190B MET* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ILE 3.5 1.2 - - - +
60B VAL* 3.2 2.7 - - - +
61B ARG* 2.4 98.9 + - + +
87B GLN* 1.3 77.1 - - - +
89B TRP* 1.3 62.8 + - - +
144B THR* 4.9 8.1 - - + +
145B VAL 3.2 15.3 - - - +
146B HIS* 3.0 28.9 + - + -
190B MET* 5.3 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PRO* 4.5 4.2 - - + +
58B VAL* 3.9 13.2 - - + -
59B ILE 3.6 16.6 - - - +
60B VAL* 4.0 7.9 - - + -
87B GLN* 3.8 25.1 - - + -
88B GLU* 1.3 82.8 - - - +
90B SER* 1.3 76.7 + - - +
91B ASP* 4.3 4.0 - - - +
114B ILE* 4.2 3.3 - - + +
115B TRP* 3.3 53.9 + + - -
116B ILE* 4.0 10.3 - - + -
117B PRO* 3.7 23.8 - - + -
144B THR* 3.6 6.2 - - - +
145B VAL* 3.1 53.3 + - + +
147B TRP* 3.9 25.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PRO* 3.7 17.7 - - - +
53B ASN* 4.0 9.2 + - - -
58B VAL* 4.8 4.8 - - - +
59B ILE 4.6 2.0 + - - +
89B TRP* 1.3 82.1 - - - +
91B ASP* 1.3 59.3 + - - +
92B TYR 3.8 0.7 + - - -
95B ARG* 4.9 13.6 + - - -
142B THR 5.3 1.0 + - - -
143B GLY 3.4 6.2 - - - -
144B THR* 3.6 18.2 + - - +
----------------------------------------------------------
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