Contacts of the strand formed by residues 122 - 129 (chain C) in PDB entry 2P4K
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 122 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL* 3.8 7.3 - - - +
120C GLY 4.1 0.4 + - - -
121C SER* 1.3 77.9 - - - +
123C TRP* 1.3 68.6 + - - -
140C CYS 3.1 12.8 - - - -
142C ASN 3.5 12.3 - - - -
160C VAL* 2.9 31.4 + - - +
161C TRP* 3.5 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 3.4 48.0 - - + +
74C HIS* 3.9 13.0 - + - -
77C PHE* 3.7 26.5 - + + -
118C VAL* 4.2 7.5 - - - +
122C GLY* 1.3 79.3 - - - -
124C GLY* 1.3 59.9 + - - +
125C TRP* 3.4 35.5 - + + +
139C ALA* 3.3 5.5 - - - +
140C CYS* 2.8 35.1 + - + +
142C ASN 3.3 15.3 + - - -
143C GLN* 2.9 24.8 + - - -
144C ASP 5.2 2.0 - - - -
157C GLY 4.5 2.2 - - - -
158C ILE 3.4 10.3 - - - -
159C ASP* 3.5 51.4 - - + -
160C VAL* 4.1 0.4 - - - +
161C TRP* 3.8 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LEU* 3.9 8.3 - - - -
114C ALA* 5.1 1.6 - - - -
115C SER* 3.6 25.1 + - - -
123C TRP* 1.3 75.9 - - - +
125C TRP* 1.3 61.3 + - - -
138C ALA 3.8 4.0 - - - -
139C ALA* 4.4 3.8 - - - -
156C LEU 4.0 0.2 - - - +
157C GLY* 3.4 3.6 - - - -
158C ILE* 2.8 37.5 + - - +
160C VAL* 4.7 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 3.8 25.5 + - - -
76C ILE* 3.9 33.0 - - + -
77C PHE 5.4 0.2 - - - -
111C LEU* 3.7 8.7 - - - +
123C TRP* 3.4 40.3 - + + +
124C GLY* 1.3 74.9 - - - -
126C LEU* 1.3 59.5 + - - +
127C GLY 4.0 0.4 + - - +
137C ILE* 3.2 10.2 - - - +
138C ALA* 2.7 39.0 + - + +
140C CYS* 3.8 29.6 - - - +
144C ASP 5.1 1.0 + - - -
146C LEU* 3.9 34.5 - - + +
154C PRO* 3.5 28.7 - - + -
156C LEU 3.3 24.9 - - - -
157C GLY* 3.3 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 5.0 2.0 - - + -
97C ILE* 5.0 9.2 - - + -
101C PHE* 3.9 33.7 - - + -
107C PHE* 3.9 31.9 - - + -
111C LEU* 4.1 5.0 - - + +
125C TRP* 1.3 75.1 - - - +
127C GLY* 1.3 61.9 + - - +
135C LEU* 4.0 19.7 - - + -
136C GLN 3.9 3.1 - - - +
137C ILE* 4.3 2.7 - - + -
154C PRO* 4.1 1.0 - - - +
155C LEU* 2.9 46.7 + - + +
156C LEU* 2.8 25.9 + - + +
186C TRP* 5.0 1.3 - - + -
189C VAL* 4.6 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C TRP* 3.9 1.8 - - - +
126C LEU* 1.3 74.3 - - - +
128C PHE* 1.3 60.2 + - - -
135C LEU* 3.4 11.3 - - - +
136C GLN* 2.8 36.7 + - - -
146C LEU* 4.1 13.2 - - - -
152C LEU* 4.6 5.1 - - - +
153C ILE 3.1 12.3 - - - -
155C LEU* 4.0 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C GLY* 1.3 72.2 - - - -
129C ASN* 1.3 70.3 + - - +
130C LYS* 3.6 20.2 + - + -
133C GLY* 3.8 21.8 - - - -
134C HIS* 3.7 25.1 - - - -
135C LEU* 4.1 11.4 - - + -
152C LEU* 3.6 5.2 - - - -
153C ILE* 2.8 35.2 + - + +
155C LEU* 4.1 7.2 - - + +
193C TYR* 4.0 22.9 - + - -
196C CYS* 3.4 48.5 - - + -
197C LYS* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C GLY 4.2 0.4 - - - -
128C PHE* 1.3 72.3 - - - +
130C LYS* 1.3 56.2 + - - +
131C GLU* 3.0 14.0 + - - +
132C ARG* 2.9 35.0 + - - +
133C GLY* 2.8 26.5 + - - -
134C HIS* 2.9 26.6 + - + +
135C LEU* 4.8 0.2 - - - +
136C GLN* 2.9 25.9 + - + +
151C GLY 5.7 0.2 - - - -
152C LEU* 3.5 21.5 - - + +
----------------------------------------------------------
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