Contacts of the strand formed by residues 127 - 134 (chain C) in PDB entry 3K9S
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 GLY 127 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ARG* 4.0 5.4 - - - +
125C GLY 4.0 1.2 + - - -
126C SER* 1.3 76.8 - - - +
128C TRP* 1.3 65.3 + - - -
143C THR 3.2 11.9 - - - -
145C ASN 3.6 14.1 - - - -
168C VAL* 2.8 31.7 + - - +
169C TRP* 3.3 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASN* 3.4 44.1 - - + +
81C HIS* 3.7 8.7 - + - -
83C LEU* 5.7 0.4 - - + -
84C PHE* 3.8 25.6 - + + -
123C ARG* 4.4 1.2 - - - +
127C GLY* 1.3 74.6 - - - -
129C ALA* 1.3 59.0 + - - +
130C TRP* 3.4 39.7 - + + +
142C SER* 3.2 7.8 - - - -
143C THR* 3.0 31.8 + - - +
145C ASN 3.2 22.8 + - - -
146C GLN* 2.9 19.1 + - - -
147C ASP 4.5 2.9 - - - -
165C GLY 4.3 2.7 - - - -
166C LEU 3.4 15.0 - - - -
167C ASP* 3.5 39.6 + - + -
168C VAL* 4.0 4.4 - - - +
169C TRP* 4.2 0.4 - - - +
207C PEO 3.3 23.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
116C PHE* 3.8 18.1 - - + +
119C ALA* 4.4 5.6 - - + -
120C ALA* 3.7 40.4 - - + +
128C TRP* 1.3 73.3 - - - +
130C TRP* 1.3 62.8 + - - +
141C VAL 3.6 6.7 - - - +
142C SER* 4.2 1.6 - - - -
165C GLY* 3.2 3.8 - - - -
166C LEU* 2.9 36.1 + - + +
168C VAL* 4.7 1.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASN* 3.3 35.4 - - + -
83C LEU* 4.1 17.3 - - + -
116C PHE* 3.7 7.3 - - - -
128C TRP* 3.4 36.8 - + + +
129C ALA* 1.3 77.4 - - - +
131C LEU* 1.3 59.5 + - - +
132C VAL* 3.7 17.7 - - + -
139C ALA 3.7 0.3 - - - +
140C VAL* 3.3 10.6 - - - +
141C VAL* 2.8 45.0 + - + +
142C SER* 4.2 2.5 - - - -
143C THR* 3.0 22.8 + - + -
147C ASP 4.0 4.7 - - - -
148C SER* 4.7 1.6 - - - -
149C PRO* 3.5 28.0 - - + +
162C PRO* 3.8 23.3 - - + -
164C MET 3.5 19.5 - - - +
165C GLY* 3.8 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 4.8 4.0 - - + -
102C ILE* 4.4 17.5 - - + -
106C PHE* 4.0 21.1 - - + -
112C PHE* 3.8 30.7 - - + -
116C PHE* 3.8 2.4 - - - -
130C TRP* 1.3 72.3 - - - +
132C VAL* 1.3 54.2 + - - +
138C LEU* 4.0 17.7 - - + -
139C ALA 3.4 13.0 - - - +
140C VAL* 4.8 0.7 - - - +
162C PRO* 3.6 1.6 - - - +
163C ILE* 2.7 55.1 + - + +
164C MET* 3.1 36.4 + - + +
194C TRP* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C TRP* 3.7 22.0 - - + -
131C LEU* 1.3 77.9 - - - +
133C LEU* 1.3 60.6 + - - +
134C LYS* 4.0 11.9 - - + -
138C LEU* 3.2 11.6 - - - +
139C ALA* 2.8 54.9 + - + +
141C VAL* 3.7 15.0 - - + -
149C PRO* 3.8 22.0 - - + -
159C SER 3.7 17.7 - - - +
160C GLY 4.2 3.8 - - - -
161C PHE 3.4 7.0 - - - +
162C PRO* 4.2 5.4 - - + -
163C ILE* 4.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 1.3 71.1 - - - +
134C LYS* 1.3 60.3 + - - +
135C GLY 3.4 24.6 + - - +
136C ASP* 3.9 4.9 - - - -
137C LYS 3.7 24.9 - - - +
138C LEU* 3.9 13.0 - - + +
160C GLY* 3.7 1.0 - - - -
161C PHE* 2.9 40.9 + - + +
163C ILE* 4.1 13.0 - - + +
201C PHE* 4.3 17.7 - - + -
204C LYS* 3.9 41.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 3.9 14.8 - - + -
133C LEU* 1.3 69.7 - - - +
135C GLY* 1.3 59.8 + - - +
136C ASP* 3.2 1.2 + - - +
137C LYS* 2.8 33.9 + - + +
139C ALA* 4.1 13.1 - - + +
141C VAL* 4.2 15.5 - - - +
153C GLU* 4.6 7.5 + - - +
158C ALA* 6.2 0.2 - - - +
159C SER* 3.5 40.4 - - - +
160C GLY* 3.8 9.2 - - - -
----------------------------------------------------------
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