Contacts of the strand formed by residues 120 - 128 (chain C) in PDB entry 5SWW
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 VAL 120 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 3.8 20.2 - - + -
90C TYR* 3.5 7.4 - - + +
92C VAL* 3.7 28.0 - - + -
113C PHE* 3.8 33.2 - - + -
114C LEU* 3.8 16.7 - - + +
117C ASN* 3.5 11.7 + - + +
118C THR 3.2 2.4 - - - +
119C HIS* 1.3 107.0 - - + +
121C ARG* 1.3 74.9 + - - +
122C LEU* 4.8 1.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 5.9 2.5 - - + -
89C ILE* 4.3 18.1 - - + +
90C TYR 2.9 12.1 + - - +
91C ARG* 3.4 11.9 - - + +
92C VAL* 2.9 25.6 + - - +
114C LEU* 5.1 0.2 - - - -
118C THR 4.3 12.3 + - - -
120C VAL* 1.3 83.7 - - - +
122C LEU* 1.3 60.9 + - - +
147C GLY* 4.6 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C PHE* 5.8 0.2 - - + -
91C ARG* 6.1 0.2 - - - -
92C VAL* 3.5 35.2 - - + +
94C TRP* 3.9 27.1 - - + +
110C VAL* 3.7 29.8 - - + -
113C PHE* 6.2 1.8 - - + -
114C LEU* 3.9 20.4 - - + +
120C VAL* 4.3 2.4 + - + -
121C ARG* 1.3 74.1 - - - +
123C ARG* 1.3 70.3 + - - +
124C ILE* 3.8 22.9 - - + -
147C GLY 4.1 3.9 + - - +
148C ALA* 3.1 17.3 - - + +
149C GLN* 3.1 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ARG* 3.5 46.0 - - + +
92C VAL 2.9 17.4 + - - +
93C THR* 3.4 30.4 + - + +
94C TRP* 2.9 28.1 + - - +
122C LEU* 1.3 74.5 - - - +
124C ILE* 1.3 62.5 + - - +
125C PHE* 3.7 17.9 - - + -
149C GLN* 3.5 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C TRP* 3.9 24.2 - - + -
96C ILE* 4.0 23.6 - - + -
100C PRO* 4.3 12.8 - - + -
122C LEU* 3.8 29.8 - - + -
123C ARG* 1.3 75.3 - - - +
125C PHE* 1.3 67.6 + - - +
126C ALA* 4.6 3.4 - - + +
143C LEU* 3.7 37.9 - - + -
148C ALA* 4.7 4.5 - - + -
149C GLN* 2.7 16.7 + - - +
150C VAL* 4.8 7.8 - - + +
151C SER* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C THR* 4.0 7.2 - - + -
94C TRP 2.9 22.2 + - - +
95C PHE* 3.4 29.8 - + + -
96C ILE* 2.9 28.6 + - - +
123C ARG* 3.7 33.7 - - + -
124C ILE* 1.3 73.4 - - - +
126C ALA* 1.3 59.7 + - - +
149C GLN* 3.7 19.1 - - - -
151C SER* 3.6 31.0 - - - -
152C ILE 4.6 4.3 - - - -
153C MET* 3.7 10.5 - - + +
157C GLU* 3.8 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ILE* 3.5 9.9 - - + -
99C SER* 4.0 24.9 - - - +
124C ILE* 4.0 5.1 - - + -
125C PHE* 1.3 72.1 - - - +
127C ALA* 1.3 64.3 + - - +
128C ARG 3.6 17.0 - - - +
140C LEU* 5.9 2.0 - - + -
150C VAL* 6.2 2.2 - - + -
151C SER 3.1 13.0 + - - +
152C ILE* 3.5 16.9 - - + +
153C MET* 2.9 20.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 3.9 20.6 - - + +
24C ASN* 3.2 22.6 + - + +
96C ILE 3.0 11.2 + - - +
97C SER* 3.7 10.1 - - - +
126C ALA* 1.3 73.9 - - - +
128C ARG* 1.3 63.8 + - + +
152C ILE* 4.7 2.8 - - - +
153C MET* 3.7 27.4 - - - +
158C PHE* 3.9 16.4 - - + -
186C LEU* 3.3 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ASN* 2.3 26.8 + - - +
22C PHE* 4.2 1.2 - - - +
23C ASN 2.8 31.5 + - - +
24C ASN* 3.6 24.9 - - - +
25C GLY 5.2 0.9 - - - -
26C ILE 3.2 16.7 + - - -
27C GLY* 3.6 4.5 - - - -
28C ARG* 3.8 8.3 - - - +
30C LYS 4.3 2.4 + - - -
97C SER* 2.5 34.5 + - - +
98C TRP* 3.0 55.2 - - + +
99C SER 3.1 23.3 + - - -
126C ALA* 3.6 10.1 - - - +
127C ALA* 1.3 78.4 - - + +
129C ILE* 1.3 64.3 + - - +
152C ILE* 5.3 0.2 - - - -
186C LEU* 3.7 7.2 - - + -
----------------------------------------------------------
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