Contacts of the strand formed by residues 121 - 128 (chain C) in PDB entry 3DC6
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 121 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C VAL* 3.9 8.2 - - - +
119C GLY 3.9 1.6 + - - -
120C SER* 1.3 77.5 - - - +
122C TRP* 1.3 69.9 + - - -
139C CYS 3.2 12.3 - - - -
141C ASN 3.7 10.5 - - - -
159C VAL* 2.8 31.3 + - - +
160C TRP* 3.4 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 3.4 41.2 - - + +
74C HIS* 3.8 15.9 - + - -
77C PHE* 3.6 32.1 - + + -
117C VAL* 4.2 5.6 - - - +
121C GLY* 1.3 76.5 - - - -
123C GLY* 1.3 59.1 + - - +
124C TRP* 3.4 38.5 - + - +
138C THR* 3.2 7.9 - - - -
139C CYS* 2.9 37.4 + - + +
141C ASN 3.3 22.3 + - - -
142C GLN* 3.0 20.0 + - - -
157C ILE 3.4 12.6 - - - -
158C ASP* 3.5 52.9 + - + -
159C VAL* 4.4 0.9 - - - -
160C TRP* 4.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 3.9 7.2 - - - +
114C THR* 3.3 26.9 + - - +
122C TRP* 1.3 73.5 - - - +
124C TRP* 1.3 61.4 + - - -
137C ALA 3.6 5.6 - - - -
138C THR* 4.2 5.2 - - - -
155C PHE 3.9 0.2 - - - +
156C GLY* 3.2 4.0 - - - -
157C ILE* 2.9 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 4.0 23.6 + - - -
76C ILE* 3.6 39.0 - - + -
77C PHE 5.1 0.7 - - - -
80C ASN* 4.7 0.2 - - - -
110C LEU* 3.5 10.6 - - - +
122C TRP* 3.4 44.8 - + + +
123C GLY* 1.3 75.5 - - - -
125C LEU* 1.3 59.0 + - - +
135C LYS 3.7 0.2 - - - +
136C VAL* 3.4 5.7 - - - -
137C ALA* 2.7 39.5 + - + +
139C CYS* 3.8 28.2 - - - +
143C ASP 5.1 0.4 + - - -
145C LEU* 3.7 35.4 - - + +
153C PRO* 3.7 21.3 - - + -
155C PHE 3.3 12.6 - - - -
156C GLY* 3.2 32.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 5.1 4.3 - - + -
96C ILE* 5.1 0.2 - - + -
100C PHE* 4.1 16.8 - - + -
106C LEU* 3.9 36.1 - - + -
110C LEU* 4.0 15.3 - - + +
124C TRP* 1.3 74.0 - - - +
126C GLY* 1.3 59.6 + - - +
134C LEU* 4.4 16.6 - - + -
135C LYS 3.6 8.5 - - - +
136C VAL* 4.8 2.5 - - + +
153C PRO* 4.0 2.1 - - - +
154C LEU* 3.0 46.9 + - + -
155C PHE* 2.8 22.7 + - + +
180C TRP* 6.3 0.2 - - + -
185C TRP* 4.9 7.9 - - + -
188C VAL* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C TRP* 3.8 1.2 - - - +
125C LEU* 1.3 73.2 - - - +
127C TYR* 1.3 60.8 + - - -
134C LEU* 3.5 10.1 - - - +
135C LYS 2.7 40.0 + - - -
137C ALA* 6.2 0.2 - - - +
145C LEU* 4.3 10.8 - - - -
151C LEU* 4.5 9.4 - - - -
152C VAL 3.2 12.8 - - - -
154C LEU* 4.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ALA* 6.3 0.4 - - + -
126C GLY* 1.3 74.3 - - - +
128C CYS* 1.3 70.6 + - - +
129C PRO* 3.3 21.0 + - + +
132C LYS* 3.4 44.1 - - - +
133C ILE 3.8 9.6 - - - -
134C LEU* 3.8 10.5 - - + -
151C LEU* 3.6 3.4 - - - -
152C VAL* 2.8 36.5 + - + +
154C LEU* 4.2 7.4 - - + -
192C PHE* 3.8 26.2 - + + -
195C ALA* 3.5 47.6 - - + -
196C GLN* 3.9 23.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C TYR* 1.3 74.0 - - - +
129C PRO* 1.3 66.9 - - - +
130C LYS* 3.9 7.9 - - - -
131C GLY* 3.4 22.9 - - - -
132C LYS* 2.9 29.5 + - - -
133C ILE* 2.9 30.4 + - + +
135C LYS* 3.7 20.6 - - + +
150C GLY 6.4 0.2 - - - -
151C LEU* 3.5 19.4 - - + +
----------------------------------------------------------
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