Contacts of the strand formed by residues 69 - 84 (chain A) in PDB entry 4IYT
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 ILE 69 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN* 4.0 2.1 - - - +
63A TYR* 3.0 57.2 + - + +
66A THR* 3.5 17.0 + - + +
67A ASP* 5.2 1.2 - - - -
68A HIS* 1.4 109.4 + - + +
70A LYS* 1.3 66.8 + - - +
238A HIS* 4.2 18.2 - - + -
239A ALA 3.5 3.4 - - - +
240A THR* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR 3.8 3.4 - - - -
62A ASN* 4.3 8.7 - - + +
63A TYR 5.0 0.4 - - - -
67A ASP 5.7 2.7 - - - +
68A HIS 5.3 0.2 - - - -
69A ILE* 1.3 79.1 - - - +
71A ALA* 1.3 60.9 + - - +
186A GLN* 4.9 3.4 - - + +
188A PRO* 3.9 32.8 - - + +
191A TYR* 3.6 45.1 - - + -
192A PHE* 3.2 3.3 - - + -
238A HIS* 3.4 3.0 - - - +
239A ALA 2.7 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR 3.9 0.2 - - - +
60A TYR* 3.2 8.0 - - - +
61A TYR* 2.8 70.3 + - + +
63A TYR* 4.8 2.0 - - + +
70A LYS* 1.3 74.5 - - - +
72A MET* 1.3 60.1 + - - +
73A ARG 4.2 0.2 - - - -
188A PRO 4.8 0.3 - - - +
192A PHE* 3.6 5.4 - - - -
236A VAL* 4.0 3.1 - - + -
237A THR 3.3 4.7 - - - +
238A HIS* 3.6 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 4.0 2.9 - - + -
59A THR 3.4 4.9 - - - +
60A TYR* 3.5 37.5 - - + +
71A ALA* 1.3 72.8 - - - +
73A ARG* 1.4 59.6 + - - +
74A TRP* 3.6 19.5 - - + -
178A PHE* 3.6 46.4 - - + -
192A PHE* 3.6 26.0 - - + -
198A LEU* 4.3 5.2 - - + -
202A VAL* 3.6 25.8 - - + -
236A VAL* 3.4 3.5 - - - -
237A THR* 2.8 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS 4.9 1.2 + - - -
58A THR* 3.1 6.8 - - - +
59A THR* 2.7 71.6 + - - +
61A TYR* 4.1 29.5 + - + -
71A ALA 4.2 0.4 - - - -
72A MET* 1.4 70.3 - - - +
74A TRP* 1.3 61.2 + - - +
234A MET* 3.9 27.9 - - + +
235A ASP 3.4 11.4 - - - +
236A VAL* 3.9 12.8 - - + -
260A PHE* 4.1 26.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 3.9 4.5 - - - +
72A MET* 3.6 46.0 - - + -
73A ARG* 1.3 73.7 - - - +
75A PRO* 1.4 87.2 - - + +
76A PHE* 3.2 22.1 + + - -
142A TYR* 3.7 12.1 - - - -
160A ALA* 3.8 21.5 - - + -
177A LEU* 4.0 6.5 - - + -
178A PHE* 3.7 31.7 - + - -
202A VAL* 4.2 4.0 - - + -
234A MET* 3.4 7.8 - - - -
235A ASP* 2.9 45.8 + - + +
237A THR* 3.0 21.2 + - - +
255A ARG* 3.4 37.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 3.5 17.5 - - - +
58A THR* 3.3 17.9 - - - +
74A TRP* 1.4 85.2 - - + +
76A PHE* 1.3 61.4 + - - +
77A GLN 3.1 2.9 + - - +
78A TYR* 3.4 36.1 - - + +
142A TYR* 2.7 30.9 + - - +
201A LEU 3.4 11.2 - - - +
202A VAL* 4.6 2.7 - - - +
232A ARG* 4.1 11.0 - - + -
233A ASN 3.5 7.4 - - - +
234A MET* 3.8 9.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 3.2 17.0 + + + -
75A PRO* 1.3 73.2 - - - +
77A GLN* 1.3 67.3 + - + +
142A TYR* 3.6 1.0 - - - -
159A LYS* 3.2 36.3 - - + -
160A ALA* 2.8 48.7 + - + -
172A GLY 3.5 27.4 - - - -
173A HIS* 4.7 5.2 - - + -
233A ASN* 2.9 11.5 + - + +
235A ASP* 3.4 29.6 - - - +
255A ARG* 4.0 1.8 - - - -
257A HIS* 3.4 36.1 - + - -
258A ASN* 4.7 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO* 3.1 2.0 - - - +
76A PHE* 1.3 94.2 - - + +
78A TYR* 1.3 74.9 + - - +
79A ASN* 2.9 21.4 + - - +
142A TYR* 4.7 0.2 - - - -
147A GLU* 3.2 29.3 + - - +
157A GLY* 3.7 13.7 - - - -
158A ILE 3.3 12.6 - - - +
159A LYS* 3.7 23.9 - - + +
232A ARG* 3.3 6.2 - - - +
233A ASN* 2.8 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 3.7 43.3 - - + -
55A ASN 4.3 0.2 - - - -
56A SER* 3.3 10.2 - - - -
75A PRO* 3.4 13.4 - - + +
77A GLN* 1.3 79.6 - - - +
79A ASN* 1.3 61.7 + - - +
142A TYR* 4.3 5.4 - + - -
157A GLY* 3.5 2.9 - - - -
158A ILE* 2.8 47.0 + - + +
201A LEU* 2.5 53.0 + - + -
205A GLY* 3.3 14.4 - - - -
206A PHE* 3.7 37.7 - - + -
231A GLY 3.3 7.4 - - - +
232A ARG* 3.8 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 4.0 0.5 - - - +
77A GLN* 2.9 31.0 + - - +
78A TYR* 1.3 73.8 - - - +
80A ILE* 1.3 65.7 + - - +
147A GLU* 4.3 0.5 - - - +
155A GLN* 3.7 22.7 + - - +
156A TRP 3.7 3.8 - - - -
229A THR* 4.2 2.9 - - + +
230A TYR* 3.3 5.2 - - - -
231A GLY 2.8 30.1 + - - +
232A ARG 3.6 11.1 - - - +
233A ASN* 3.0 24.7 + - - +
262A ASN* 3.9 4.0 + - - -
264A ASN* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 4.6 9.0 - - + -
54A ILE* 3.5 23.8 - - + -
79A ASN* 1.3 82.1 - - - +
81A GLY* 1.3 58.2 + - - +
155A GLN* 3.3 4.1 - - - -
156A TRP* 2.8 57.9 + - + +
158A ILE* 3.8 14.6 - - + -
206A PHE* 4.2 2.2 - - + -
208A PRO* 3.6 19.1 - - + -
210A PHE* 3.7 38.4 - - + -
229A THR 3.4 2.5 - - - -
230A TYR* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 5.2 0.9 - - - -
80A ILE* 1.3 78.1 - - - +
82A LEU* 1.3 59.9 + - - -
154A VAL 3.4 8.7 - - - -
155A GLN* 3.4 17.7 - - - -
156A TRP* 5.2 0.7 - - - -
227A GLU 4.4 0.4 - - - -
228A ILE* 3.2 10.4 - - - +
229A THR* 2.8 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.3 17.5 - - + -
50A MET* 4.2 15.7 - - + -
81A GLY* 1.3 74.4 - - - +
83A LYS* 1.3 68.4 + - - +
91A LEU* 4.5 10.1 - - + -
152A LYS 5.7 0.2 - - - +
153A SER* 3.1 7.2 - - - -
154A VAL* 2.9 41.0 + - + +
156A TRP* 5.5 0.4 - - + -
212A ALA* 3.4 32.1 - - + -
214A VAL* 4.9 5.2 - - + -
226A PHE* 3.8 29.2 - - + -
227A GLU 3.4 2.7 - - - +
228A ILE* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 1.3 78.9 - - - +
84A THR* 1.3 71.0 + - - +
85A ASN* 6.1 1.8 - - + -
152A LYS* 3.3 6.5 - - + +
153A SER* 3.9 15.0 - - - -
226A PHE* 3.2 7.3 - - - -
227A GLU* 2.8 68.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 1.3 83.1 - - - +
85A ASN* 1.3 58.3 + - - +
86A ASP* 3.2 17.3 + - - +
89A VAL* 3.7 27.8 - - + +
152A LYS* 2.8 51.4 + - + +
214A VAL* 5.6 1.3 - - + -
224A SER* 4.7 0.2 - - - -
225A GLU 2.8 23.1 + - - -
226A PHE* 3.7 17.4 - - + -
301A MES 4.2 3.3 - - - +
----------------------------------------------------------
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