Contacts of the strand formed by residues 93 - 100 (chain A) in PDB entry 4IQJ
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 TYR 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 3.4 37.2 - + + -
75A VAL 3.3 12.6 - - - +
76A ALA* 4.5 1.1 - - - +
77A ALA 4.6 0.4 - - - +
92A GLY* 1.3 81.8 - - - +
94A PHE* 1.3 77.3 + - - +
95A HIS* 4.5 9.4 - + - -
122A TYR* 6.5 0.7 - + - -
123A GLU* 3.7 25.5 + - + +
124A LYS* 3.7 36.6 + - + +
126A ARG* 3.8 28.0 - - + -
147A GLY 4.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 3.2 4.5 - - - -
75A VAL* 2.3 53.0 + - + +
76A ALA 4.9 1.1 - - - -
77A ALA* 4.4 25.4 - - + -
92A GLY 6.0 1.3 - - - -
93A TYR* 1.3 84.7 - - - +
95A HIS* 1.3 64.1 + - - +
147A GLY 3.5 15.9 - - - -
148A ALA 3.6 0.7 - - - -
149A GLU* 3.5 44.2 - - + +
152A GLN* 3.6 35.7 - - + -
153A PHE* 4.9 17.9 - + - -
165A ARG* 5.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A HIS* 3.7 22.9 - + - -
72A GLU* 2.8 30.1 + - + +
73A ALA 3.5 4.5 - - - -
74A TYR* 3.5 28.2 - + - -
75A VAL* 4.5 0.3 - - - +
93A TYR* 4.5 9.2 - + - -
94A PHE* 1.3 80.5 - - - +
96A LEU* 1.3 65.2 + - - +
144A GLY* 5.4 0.2 - - - -
145A CYS* 3.9 14.5 - - - +
147A GLY* 3.1 30.2 + - - +
148A ALA* 3.1 25.3 - - + +
149A GLU* 4.0 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR 3.5 0.9 - - - +
72A GLU* 4.3 4.7 - - - +
73A ALA* 2.8 37.2 + - + +
75A VAL* 3.4 26.0 - - + -
95A HIS* 1.3 80.2 - - - +
97A THR* 1.3 60.9 + - - +
98A LEU* 3.7 17.3 + - + +
127A ILE* 5.5 0.7 - - + -
132A LEU* 3.5 32.1 - - + -
141A ALA* 5.2 1.6 - - + -
142A LEU 3.3 24.2 - - - +
143A SER* 4.5 8.7 - - - +
144A GLY* 5.0 3.8 - - - -
148A ALA* 5.5 0.4 - - + -
149A GLU* 4.2 13.9 - - + +
169A ASP* 4.9 8.5 - - - +
173A PHE* 5.2 2.0 - - + -
177A PHE* 5.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 4.5 4.0 - - - +
11A HIS* 3.0 37.2 + - + +
45A THR* 4.1 24.7 - - + -
71A TYR 4.1 2.0 - - - -
72A GLU* 4.3 4.0 - - - +
96A LEU* 1.3 72.9 - - - +
98A LEU* 1.3 72.0 + - - +
99A LEU* 4.6 3.1 - - + -
140A ILE 4.1 0.2 - - - +
141A ALA* 3.5 0.2 - - - -
142A LEU* 3.0 48.0 + - + +
144A GLY* 4.1 5.5 - - - -
180A GLU* 3.1 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLY* 3.2 3.8 - - - -
71A TYR* 2.8 44.8 + - + +
73A ALA* 4.1 20.2 - - + -
96A LEU* 4.0 20.0 - - + +
97A THR* 1.3 86.0 - - - +
99A LEU* 1.3 63.5 + - - +
109A LEU* 4.0 14.2 - - + +
112A LEU* 4.0 15.3 - - + -
127A ILE* 5.3 0.2 - - + -
132A LEU* 3.6 23.6 - - + -
139A LEU* 4.2 7.6 - - + -
140A ILE 3.6 2.5 - - - +
141A ALA* 3.9 21.3 - - + -
173A PHE* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.7 55.6 - - + +
43A ALA* 4.0 11.9 - - + -
45A THR* 4.0 11.9 - - + -
68A ILE* 4.0 10.8 - - + -
69A ILE 4.2 1.3 - - - -
70A GLY* 4.0 7.0 - - - -
97A THR* 4.6 6.5 - - + -
98A LEU* 1.3 80.8 - - - +
100A ALA* 1.3 61.6 + - - +
101A LYS 3.4 0.5 + - - -
109A LEU* 4.4 2.7 - - - -
139A LEU* 3.6 5.0 - - - -
140A ILE* 2.7 47.9 + - + +
142A LEU* 4.7 15.9 - - + -
277A ILE* 4.5 12.1 - - + -
281A CYS* 4.8 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 4.6 2.4 - - - +
69A ILE* 3.1 30.3 + - + +
99A LEU* 1.3 70.4 - - - +
101A LYS* 1.3 63.3 + - - +
106A TYR* 4.1 17.3 - - - +
109A LEU* 3.6 16.2 - - + +
138A GLY 3.9 4.7 - - - -
139A LEU* 4.4 1.1 - - - -
281A CYS* 3.4 18.6 - - - +
283A VAL* 3.5 24.8 - - + +
----------------------------------------------------------
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