Contacts of the strand formed by residues 70 - 81 (chain B) in PDB entry 1XFS
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 70 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 3.0 22.6 + - - +
62B VAL* 3.7 20.4 - - + -
63B MSE 3.2 4.5 - - - +
64B GLN* 2.7 29.9 + - - +
68B GLY 3.5 8.9 + - - +
69B ASN* 1.3 74.8 - - - +
71B PHE* 1.3 73.5 + - - +
72B PRO* 4.0 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 3.9 32.3 - + - -
62B VAL* 4.4 0.7 - - - -
63B MSE 2.6 47.4 + - + +
65B ASP* 4.5 7.9 - - - -
69B ASN* 4.1 28.7 - - + -
70B LYS* 1.3 79.4 - - - +
72B PRO* 1.3 66.1 - - + +
73B ASN* 2.8 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR* 3.9 24.9 - - + +
61B THR 3.5 7.0 - - - +
62B VAL* 4.4 5.6 - - + -
70B LYS* 4.0 8.7 - - + +
71B PHE* 1.3 88.0 - - + +
73B ASN* 1.3 65.9 + - - +
74B SER* 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PHE 3.9 1.1 - - - +
60B TYR* 3.5 5.9 - - - -
61B THR* 2.8 50.6 + - - +
63B MSE 4.5 18.4 - - - +
71B PHE* 2.8 30.3 - - - +
72B PRO* 1.3 76.7 - - - +
74B SER* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 5.7 0.8 + - - -
59B PHE 3.7 3.8 - - - -
60B TYR* 3.5 22.9 - - - +
72B PRO* 5.6 0.5 - - - +
73B ASN* 1.3 72.7 - - - +
75B GLY* 1.3 58.8 + - - +
90B SER* 4.3 14.3 - - - +
92B LEU 4.2 1.4 - - - +
93B VAL* 3.8 31.4 - - - +
94B LYS 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 3.7 5.9 - - - +
59B PHE* 2.8 36.9 + - - -
74B SER* 1.3 75.4 - - - +
76B CYS* 1.3 62.7 + - - +
88B TRP* 5.3 4.5 - - - -
89B THR 3.2 14.4 - - - -
90B SER* 4.4 2.0 - - - -
92B LEU 3.4 6.1 - - - -
93B VAL* 3.8 6.9 - - - -
94B LYS 3.9 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY* 3.7 19.1 - - - -
57B GLY 3.4 4.7 - - - -
59B PHE* 4.4 1.7 - - - +
75B GLY* 1.3 73.9 - - - -
77B PHE* 1.3 76.6 + - - +
78B LEU* 4.6 1.3 - - - -
88B TRP* 3.2 4.2 - - - +
89B THR* 2.9 35.1 + - + +
92B LEU* 3.5 16.4 - - + +
93B VAL 3.3 26.9 - - - +
96B TYR* 3.6 26.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU 5.4 4.3 - - - -
51B VAL* 3.7 29.2 - - + -
52B ASP 3.5 18.2 - - - -
53B LEU* 4.2 10.5 - - + -
54B ARG 3.3 20.4 - - - +
55B PRO* 4.2 0.4 - - - -
56B GLY 2.8 27.1 + - - -
57B GLY 2.9 14.8 + - - -
58B GLU 3.6 8.7 - - - -
59B PHE* 3.6 37.0 - + + -
76B CYS* 1.3 77.8 - - - +
78B LEU* 1.3 59.7 + - - +
80B VAL* 4.5 5.2 - - + -
86B LEU* 3.8 39.5 - - + -
87B ILE 3.6 3.4 - - - +
88B TRP* 3.8 19.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PRO* 5.6 1.0 - - - +
78A LEU* 4.2 11.8 - - + +
92A LEU* 4.0 4.7 - - + -
96A TYR* 3.6 51.0 + - + -
55B PRO* 3.6 20.4 - - - +
76B CYS* 4.0 3.6 - - - +
77B PHE* 1.3 81.3 - - - +
79B GLU* 1.3 59.5 + - - +
87B ILE* 2.7 29.4 + - + +
89B THR* 3.7 31.6 - - + +
92B LEU* 4.1 16.2 - - + -
96B TYR* 3.8 27.1 + - + -
115B THR* 4.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 4.7 11.5 + - - +
55B PRO* 4.5 4.0 - - - -
77B PHE 3.8 0.6 - - - -
78B LEU* 1.3 81.2 - - - +
80B VAL* 1.3 69.8 + - - +
81B THR* 2.9 24.1 + - - +
85B ARG* 3.0 38.2 + - - +
86B LEU* 3.5 4.7 - - - +
87B ILE* 3.0 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TRP* 3.7 24.2 - - + -
53B LEU* 3.8 25.4 - - + +
54B ARG* 3.9 33.4 - - - +
55B PRO* 4.3 10.1 - - + +
77B PHE* 4.5 6.7 - - + -
79B GLU* 1.3 82.3 - - - +
81B THR* 1.3 61.5 + - - +
82B ASP 4.0 3.0 + - - +
85B ARG 3.9 2.2 - - - -
86B LEU* 4.2 10.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
26B TRP* 3.5 2.8 - - - -
79B GLU* 2.9 26.9 + - - +
80B VAL* 1.3 73.4 + - - +
82B ASP* 1.3 68.9 + - - +
83B GLU 3.2 1.0 + - - -
84B LYS* 2.8 37.2 + - + -
85B ARG* 2.9 30.7 + - - +
----------------------------------------------------------
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