Contacts of the strand formed by residues 139 - 148 (chain C) in PDB entry 2PQA
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 LYS 139 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU 3.2 14.9 + - - +
55C LEU* 3.1 23.0 + - + +
57C ALA* 2.3 53.9 + - - +
64C PHE* 4.4 15.8 - - + -
102C MET* 4.1 24.5 - - + +
103C ASP* 4.9 4.2 + - - +
132C LEU* 4.5 9.4 - - + -
133C ARG 3.5 7.0 - - - +
134C SER* 4.3 11.0 - - - +
137C ASN* 5.0 8.5 - - - +
138C LYS* 1.3 82.3 - - - +
140C SER* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C MET* 4.1 7.0 - - - +
103C ASP* 3.4 28.7 - - - -
105C ARG* 5.2 9.8 + - - -
132C LEU* 3.7 4.4 - - - +
133C ARG* 2.8 41.6 + - - +
138C LYS* 4.8 2.4 + - - -
139C LYS* 1.3 78.7 - - - +
141C LEU* 1.3 68.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 3.6 31.4 - - + -
74C VAL* 5.1 8.5 - - + +
76C ILE* 3.8 38.1 - - + +
102C MET* 4.1 6.0 - - - -
103C ASP 3.0 7.3 + - - -
104C VAL* 3.4 21.0 - - + -
105C ARG* 2.9 28.9 + - - +
128C VAL* 4.6 9.9 - - + +
130C GLY 4.9 8.7 - - - +
131C HIS 3.5 5.2 - - - +
132C LEU* 3.8 25.4 - - + +
133C ARG* 5.5 0.2 - - - -
140C SER* 1.3 84.8 + - - +
142C VAL* 1.3 61.6 + - - +
143C ALA 3.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ARG* 4.0 10.1 - - + -
107C TRP* 3.3 35.2 - - + -
130C GLY* 3.0 3.0 - - - -
131C HIS* 2.7 62.6 + - + +
133C ARG* 4.0 21.5 - - + +
140C SER 4.1 0.2 + - - -
141C LEU* 1.3 72.5 - - - +
143C ALA* 1.3 59.4 + - - +
144C PHE* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C VAL* 3.7 19.7 - - + -
105C ARG 2.8 22.2 + - - +
106C GLN* 3.3 14.1 - - - +
107C TRP* 4.1 11.8 - - - -
128C VAL* 3.9 7.9 - - + -
129C ALA 3.6 4.7 - - - +
130C GLY* 4.0 1.1 - - - -
141C LEU 3.8 0.8 - - - -
142C VAL* 1.3 74.3 - - - +
144C PHE* 1.3 64.5 + - - +
146C ILE* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLN* 4.5 8.7 + - - +
129C ALA* 2.8 11.1 + - + +
130C GLY* 4.2 12.3 - - - -
131C HIS* 3.6 38.1 - + - -
142C VAL* 4.4 12.1 - - + -
143C ALA* 1.3 78.7 - - - +
145C LYS* 1.3 63.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 3.6 29.1 - - - +
98B LEU* 5.1 22.8 - - - +
106C GLN* 4.3 1.6 - - - +
127C LYS 4.4 0.7 - - - -
128C VAL* 3.3 1.9 - - - +
129C ALA* 3.0 39.5 + - + +
143C ALA* 4.3 0.2 - - - +
144C PHE* 1.3 80.4 - - + +
146C ILE* 1.3 70.8 + - - +
147C MET* 3.7 42.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ILE* 5.1 1.3 - - + -
92C TYR* 3.6 28.3 - - + -
94C ILE* 5.2 0.4 - - + -
104C VAL* 4.3 4.9 - - + -
106C GLN* 3.5 47.6 + - + +
120C VAL* 4.8 10.2 - - + +
126C VAL* 4.1 21.8 - - + -
127C LYS 3.5 3.8 - - - -
128C VAL* 3.8 24.0 - - + -
143C ALA* 3.8 13.5 - - + -
145C LYS* 1.3 80.7 - - - +
147C MET* 1.3 60.6 + - - +
148C PRO* 3.5 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C VAL* 4.4 2.2 - - - -
127C LYS* 2.9 70.7 + - + +
129C ALA* 4.7 9.9 - - + -
145C LYS* 3.7 50.9 - - + +
146C ILE* 1.3 72.2 - - - +
148C PRO* 1.4 70.8 - - + +
149C LEU* 3.5 1.3 + - + +
154C GLU* 5.5 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ASN* 5.9 3.6 - - - +
120C VAL* 4.3 28.5 - - + -
124C THR* 4.4 11.2 - - + -
125C TYR 3.5 12.3 - - - +
126C VAL* 4.0 4.2 - - + -
146C ILE 3.5 9.9 - - - +
147C MET* 1.4 88.5 - - + +
149C LEU* 1.3 65.3 + - - +
150C GLU* 3.5 14.0 + - - +
88D LYS* 6.2 1.6 - - - +
----------------------------------------------------------
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