Contacts of the strand formed by residues 128 - 138 (chain C) in PDB entry 5IXM
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 TYR 128 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 5.5 0.5 - - - -
126C ASP* 4.1 13.7 - - - +
127C GLY* 1.3 82.6 - - - +
129C ALA* 1.3 71.4 + - - +
130C THR* 3.8 16.6 - - - -
151C PHE* 4.2 8.1 - + + -
152C GLN 3.2 15.9 - - - +
153C VAL* 3.7 15.3 - - + +
154C PHE* 3.5 14.6 - - - -
64D GLN* 5.9 0.5 + - - -
106D PHE* 6.1 0.3 - - - -
108D ASP* 3.1 36.7 + - - -
109D ASN 4.4 1.3 - - - -
110D PRO* 3.5 32.3 - - + -
113D ALA* 4.0 23.8 + - + -
116D LYS* 4.6 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C THR* 3.4 37.5 - - + +
107C ARG* 4.9 0.2 - - - -
108C VAL* 5.4 1.1 - - + -
114C PHE* 5.2 2.5 - - + -
128C TYR* 1.3 76.2 - - - +
130C THR* 1.3 61.7 + - - +
131C GLN* 4.0 0.5 + - - +
151C PHE* 3.4 8.5 - - - +
152C GLN* 2.9 47.0 + - + +
154C PHE* 4.3 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ASN* 3.0 35.9 + - - +
105C TYR 3.6 0.2 - - - -
106C THR* 2.9 27.9 + - - -
128C TYR* 3.8 18.2 - - - -
129C ALA* 1.3 73.0 - - - +
131C GLN* 1.3 64.3 + - - +
132C ILE* 3.6 30.3 - - + -
151C PHE* 3.9 12.8 - - + -
117D GLU* 5.0 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ASN 3.5 1.6 - - - -
105C TYR* 3.5 36.9 + - + -
106C THR 3.3 26.8 + - - +
107C ARG* 3.7 23.8 - - - +
129C ALA 4.6 0.9 - - - +
130C THR* 1.3 72.6 - - - +
132C ILE* 1.3 59.7 + - - +
133C PHE* 4.8 4.2 - - + -
148C SER 3.5 3.6 - - - +
150C GLN* 2.9 70.1 + - + +
151C PHE 4.5 0.7 + - - -
152C GLN* 3.9 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ASN 5.2 1.3 - - - +
103C ILE* 3.5 4.5 - - - +
104C ASN* 2.9 48.8 + - + +
105C TYR* 4.5 0.6 - - - +
130C THR* 3.6 21.3 - - + -
131C GLN* 1.3 80.5 - - - +
133C PHE* 1.3 67.3 + - - +
134C THR* 3.9 18.6 - - - +
148C SER 3.2 5.4 - - - +
149C LYS* 3.8 27.6 - - + -
150C GLN 4.7 0.7 - - - +
151C PHE* 4.5 4.0 - - + -
117D GLU* 3.6 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C TRP* 4.3 14.4 - + - -
102C ASN 3.8 2.2 - - - -
103C ILE* 3.7 39.7 - - + -
105C TYR* 3.6 42.0 - + + -
131C GLN* 4.8 2.7 - - + -
132C ILE* 1.3 78.7 - - - +
134C THR* 1.3 66.4 + - - +
146C LEU 4.6 0.2 - - - -
147C SER* 3.2 3.1 - - - -
148C SER* 2.9 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ARG* 5.0 3.1 - - + +
101C PHE* 3.5 5.0 - - - +
102C ASN* 2.9 62.6 + - - +
103C ILE* 5.2 0.9 - - - +
132C ILE* 3.9 13.1 - - - +
133C PHE* 1.3 80.5 + - - +
135C ALA* 1.3 64.6 + - - +
136C GLY 5.1 0.2 - - - +
145C THR* 3.7 24.5 - - + -
146C LEU 3.5 4.3 - - - -
147C SER* 3.3 10.9 + - - -
149C LYS* 5.5 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ARG 3.3 4.0 - - - -
101C PHE* 3.7 24.5 - - + -
134C THR* 1.3 75.7 - - - +
136C GLY* 1.3 58.2 + - - +
145C THR* 4.5 2.7 - - - -
146C LEU* 2.9 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C VAL 3.6 0.3 - - - +
99C TRP* 3.6 10.8 - - - -
100C ARG* 2.9 42.4 + - - +
101C PHE* 5.1 1.4 - - - -
134C THR* 5.1 0.8 - - - +
135C ALA* 1.3 76.4 - - - +
137C TYR* 1.3 59.9 + - - -
144C ALA 3.2 13.7 - - - -
145C THR* 4.0 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C VAL* 3.3 46.6 - - + +
99C TRP* 3.9 33.4 - + + -
100C ARG* 5.0 1.0 - - - -
136C GLY* 1.3 74.7 - - - -
138C ALA* 1.3 73.2 + - - +
139C ASN* 3.4 34.9 + - - +
142C TRP* 3.6 35.0 - + + -
143C ASN* 3.2 4.9 - - - +
144C ALA* 2.9 34.5 + - + +
145C THR* 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C VAL* 3.0 23.0 + - - +
100C ARG* 3.9 21.1 - - - +
137C TYR* 1.3 84.6 - - - +
139C ASN* 1.3 61.2 + - - +
142C TRP 3.6 6.3 - - - -
143C ASN* 3.6 14.1 - - + +
25D TYR* 3.4 38.1 - - + +
----------------------------------------------------------
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