Contacts of the strand formed by residues 136 - 148 (chain A) in PDB entry 1Q4U
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 LEU 136 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 3.8 40.9 - - + +
102A ARG* 4.3 6.8 + - - +
128A SER* 3.6 30.7 - - - -
129A LEU 3.9 4.7 - - - +
130A ARG* 3.6 25.7 - - + +
134A GLY 3.5 2.6 + - - -
135A ARG* 1.3 70.4 - - - +
137A CYS* 1.3 60.9 + - - +
138A ALA 3.6 16.2 - - - +
139A VAL* 3.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 4.3 8.2 - - + -
100A PHE* 3.7 1.2 - - - +
101A PHE* 2.7 30.8 + - - -
102A ARG* 3.0 41.2 + - - +
103A PRO 4.3 0.4 - - - -
104A VAL* 3.7 28.3 - - + -
129A LEU 2.9 12.0 + - - +
130A ARG* 4.8 0.4 - - - -
131A ASP* 3.6 24.5 - - - -
135A ARG 3.5 13.0 - - - -
136A LEU* 1.3 75.8 - - - +
138A ALA* 1.4 58.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 4.0 24.9 - - + -
98A THR* 4.4 4.0 - - + -
99A SER 3.2 15.7 - - - +
100A PHE* 4.1 14.6 - - + -
101A PHE* 4.3 3.8 - - - -
129A LEU* 2.8 38.1 + - + +
136A LEU* 3.6 3.1 - - - +
137A CYS* 1.4 79.0 - - - +
139A VAL* 1.3 69.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A HIS 3.8 1.0 - - - +
98A THR* 3.2 3.7 - - - +
99A SER* 2.9 40.2 + - - +
101A PHE* 3.6 33.7 - - + -
127A VAL 3.1 11.2 - - - +
128A SER* 4.4 3.6 - - - -
129A LEU* 4.2 2.7 - - - -
136A LEU* 3.9 19.7 - - + -
138A ALA* 1.3 81.0 - - - +
140A SER* 1.3 63.3 + - - +
141A SER* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 3.5 21.8 - - - +
96A ASN* 3.3 19.2 + - - -
97A HIS 3.2 4.9 - - - -
98A THR* 3.3 14.6 - - - -
126A ASP* 3.9 1.2 - - - -
127A VAL* 2.7 39.5 + - - +
129A LEU* 4.4 2.9 - - - -
139A VAL* 1.3 76.3 - - - +
141A SER* 1.3 62.1 + - - +
142A MET* 3.4 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER* 3.7 5.7 + - - +
96A ASN* 3.7 0.2 - - - -
97A HIS* 2.7 45.7 + - - +
124A PHE* 3.6 25.8 - - - -
125A TRP 3.8 4.5 - - - -
126A ASP* 4.1 10.1 + - - -
139A VAL* 6.1 0.3 - - - +
140A SER* 1.3 71.4 + - - +
142A MET* 1.3 61.0 + - - +
143A SER 3.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA 4.0 13.2 - - - +
73A GLU* 3.4 40.6 - - + +
76A ALA* 3.7 18.6 - - + -
93A GLY* 4.8 2.0 - - - -
95A SER 3.6 11.0 - - - +
96A ASN* 3.3 33.0 - - - -
123A TRP 3.8 0.9 - - - +
124A PHE* 3.4 7.9 - - - -
125A TRP* 2.9 38.3 + - - +
127A VAL* 4.0 10.3 - - + -
140A SER* 3.4 15.7 - - - +
141A SER* 1.3 71.5 - - - +
143A SER* 1.3 61.2 + - - +
144A ILE* 3.7 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY* 3.6 2.3 - - - -
94A GLN* 2.7 39.9 + - - +
95A SER* 2.8 32.5 + - - +
122A THR* 3.4 22.0 - - - +
123A TRP 3.7 2.9 - - - -
124A PHE* 3.9 19.5 - - - -
141A SER 3.9 0.6 + - - -
142A MET* 1.3 74.1 - - - +
144A ILE* 1.3 54.4 + - - +
145A ALA 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA* 4.1 9.4 - - + +
77A THR* 3.5 24.0 - - + +
80A THR* 3.9 25.8 - - + +
91A ALA* 3.8 14.8 - - + -
92A VAL* 3.7 17.7 - - - +
93A GLY* 3.9 4.5 - - - -
94A GLN* 5.2 0.4 - - - -
122A THR* 3.2 7.0 - - - -
123A TRP* 2.8 46.8 + - + +
125A TRP* 4.0 12.8 - - + -
142A MET* 3.7 24.2 - - + +
143A SER* 1.3 77.6 + - - +
145A ALA* 1.3 74.2 + - - +
146A VAL* 4.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A MET* 3.8 0.7 - - - +
91A ALA* 3.2 6.8 - - - -
92A VAL* 2.8 38.5 + - + +
94A GLN* 3.7 23.5 - - + +
121A THR 3.4 4.9 - - - -
143A SER 4.0 2.4 + - - -
144A ILE* 1.3 74.3 - - - +
146A VAL* 1.3 60.3 + - - +
147A ARG* 3.6 22.0 - - + +
370A 4CA 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A THR* 4.0 18.6 - - + -
84A VAL* 4.4 9.9 - - + -
89A MET* 3.4 38.2 - - + +
90A MET 3.4 4.0 - - - +
91A ALA* 4.7 0.9 - - + -
120A SER 4.1 9.9 - - - +
121A THR* 2.7 25.4 + - - +
123A TRP* 3.9 30.3 - - + +
144A ILE 4.2 5.2 - - - +
145A ALA* 1.3 77.7 - - - +
147A ARG* 1.3 81.3 + - - +
148A PRO* 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A MET* 3.0 9.0 - - - -
90A MET* 2.3 50.0 + - + +
94A GLN* 4.1 12.3 + - - +
121A THR* 2.9 43.2 + - - -
122A THR* 5.6 0.4 + - - -
145A ALA* 3.6 16.2 - - + +
146A VAL* 1.3 89.4 + - - +
148A PRO* 1.3 71.5 - - + +
370A 4CA 3.7 63.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLY 3.6 10.1 - - - +
89A MET* 3.6 17.9 - - + -
90A MET* 4.4 0.7 - - - -
146A VAL 4.8 0.2 - - - +
147A ARG* 1.3 96.3 - - + +
149A ARG* 1.3 66.8 + - - +
150A ARG* 4.5 1.0 - - - +
370A 4CA 3.0 21.9 + - - +
----------------------------------------------------------
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