Contacts of the strand formed by residues 66 - 80 (chain A) in PDB entry 1DDL
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 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 5.1 8.2 - - + +
62A TYR 3.8 12.8 - - - -
63A THR 2.9 8.0 + - - +
65A LEU* 1.3 107.5 - - + +
67A ARG* 1.3 60.9 + - - +
68A HIS 4.1 9.9 - - - +
69A ALA* 6.0 0.4 - - + -
142A LYS* 2.9 29.3 + - - +
179A LEU* 3.8 37.0 - - + +
180A SER* 3.4 32.5 - - - +
181A SER 3.5 2.5 - - - -
182A PRO* 4.0 18.8 - - + -
183A LEU* 3.7 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 1.3 73.8 - - - +
68A HIS* 1.3 59.7 + - + +
142A LYS* 3.5 15.4 - - - +
143A ALA* 3.5 24.3 - - - +
181A SER* 2.7 20.8 + - - +
182A PRO 3.7 4.9 - - - -
183A LEU* 3.8 26.5 - - + +
15B THR* 3.1 40.4 + - - +
16B LYS 3.9 9.8 + - - +
17B PRO* 3.6 20.0 - - + +
18B SER* 5.3 1.3 - - - +
97C PRO* 4.5 8.9 - - - +
99C ASN* 4.9 7.6 - - - +
136C ASN 3.0 27.9 + - - -
138C ASN 4.2 7.9 - - - +
149C ASP* 2.9 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 4.1 4.6 - - - +
67A ARG* 1.3 80.0 - - - +
69A ALA* 1.3 62.7 + - - +
70A GLN* 3.5 32.6 - - + +
140A ILE* 4.2 11.5 - - + +
142A LYS 3.3 10.8 - - - -
143A ALA* 4.0 3.8 - - + -
178A GLU 3.7 2.2 + - - +
179A LEU* 3.5 4.5 - - - -
180A SER* 3.2 47.8 + - - +
181A SER* 4.9 4.3 - - - +
16B LYS 6.0 0.4 - - - +
18B SER* 2.8 35.0 - - - +
19B LEU 3.9 15.2 + - - -
21B PRO* 5.5 2.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.7 31.9 - - + -
66A TYR* 6.0 0.4 - - + -
68A HIS* 1.3 76.3 - - - +
70A GLN* 1.3 61.9 + - - +
140A ILE* 3.6 3.1 - - - +
141A ILE* 3.1 27.0 + - + -
142A LYS* 3.0 25.7 + - + +
177A ILE* 3.7 10.8 - - + -
178A GLU 3.3 5.4 - - - -
179A LEU* 4.0 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A HIS* 3.5 22.3 - - + -
69A ALA* 1.3 75.7 - - - +
71A LEU* 1.3 70.1 + - - +
139A PRO* 3.3 15.9 - - + +
140A ILE* 3.8 24.3 - - + +
177A ILE* 4.0 4.2 - - - +
178A GLU* 2.7 62.2 + - + +
21B PRO* 4.5 14.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 4.2 25.1 - - + -
53A ILE* 4.4 7.4 - - + -
59A LEU* 5.1 3.8 - - + -
70A GLN* 1.3 79.8 + - - +
72A LYS* 1.3 59.6 + - - +
73A HIS 4.4 8.3 - - - +
74A LEU* 4.0 18.2 - - + -
134A LEU* 3.7 14.5 - - + +
139A PRO* 2.8 35.7 + - + +
141A ILE* 4.0 30.5 - - + -
151A PRO* 4.0 21.3 - - + -
176A GLN 3.7 11.9 - - - +
177A ILE* 4.4 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 4.4 13.3 + - - +
70A GLN 3.6 1.0 + - - -
71A LEU* 1.3 74.2 - - - +
73A HIS* 1.3 87.9 + - + +
134A LEU* 3.7 10.4 - - - +
176A GLN* 2.9 44.8 + - + +
178A GLU* 3.8 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 4.4 2.6 - - - +
72A LYS* 1.3 110.5 + - + +
74A LEU* 1.3 64.1 + - - +
134A LEU* 4.3 4.7 - - - -
175A GLY* 3.2 6.3 - - - -
176A GLN* 3.1 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 4.4 16.4 - - + -
53A ILE* 4.4 6.5 - - + -
71A LEU* 4.0 27.4 - - + -
73A HIS* 1.3 77.3 - - - +
75A LYS* 1.3 71.8 + - - +
95A TRP* 3.7 36.6 - - + -
131A GLU* 3.9 3.0 - - - +
132A ALA* 2.9 40.3 + - + +
134A LEU* 4.6 9.5 - - + +
151A PRO* 4.1 12.1 - - + -
173A ILE* 4.4 14.8 - - + -
174A GLN 3.4 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 1.3 78.0 - - - +
76A ALA* 1.3 62.8 + - - +
77A THR* 3.7 11.2 - - - +
95A TRP* 4.0 6.5 - - - -
129A ASP* 3.1 39.0 + - + +
130A VAL 3.6 13.5 - - - +
131A GLU* 3.8 20.0 - - + +
132A ALA 4.3 0.9 - - - +
173A ILE* 3.2 7.6 - - - +
174A GLN* 2.9 67.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 1.3 74.3 - - - +
77A THR* 1.3 66.1 + - - +
78A ILE* 5.8 0.4 - - - -
93A LEU* 4.5 8.5 - - + -
95A TRP* 4.0 18.8 - - + +
128A ILE 3.8 0.2 - - - +
129A ASP* 3.3 1.2 - - - +
130A VAL* 2.8 40.4 + - + +
153A LEU* 4.4 14.8 - - + -
171A LEU* 4.3 13.9 - - + -
172A THR 3.3 9.6 - - - +
173A ILE* 4.3 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN* 5.2 1.0 + - - -
75A LYS* 3.7 13.0 + - - +
76A ALA* 1.3 76.0 + - - +
78A ILE* 1.3 66.2 + - - +
79A HIS* 3.4 28.2 - - + +
127A PRO* 3.7 21.3 - - + -
128A ILE 3.2 12.1 - - - +
129A ASP* 2.9 22.5 + - - +
170A TYR 3.5 0.7 - - - +
171A LEU* 3.4 5.9 - - - +
172A THR* 2.9 36.0 + - - -
174A GLN* 5.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 5.8 1.1 - - + -
76A ALA 5.8 0.2 - - - -
77A THR* 1.3 77.7 - - - +
79A HIS* 1.3 61.7 + - - +
80A PRO* 3.6 3.9 - - - +
91A VAL* 3.7 27.8 - - + -
93A LEU* 4.1 11.0 - - + -
116A PHE* 4.0 27.4 - - + -
118A ILE* 3.9 25.4 - - + -
127A PRO* 3.4 15.9 - - - +
128A ILE* 2.9 28.5 + - + +
130A VAL* 5.7 1.6 - - + -
169A CYS* 4.0 26.0 - - + -
170A TYR 3.4 5.2 - - - +
171A LEU* 4.3 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN* 3.6 13.8 + - - -
77A THR* 3.4 20.1 - - + +
78A ILE* 1.3 76.6 - - - +
80A PRO* 1.3 68.0 - - + +
81A THR* 5.1 0.2 - - - -
127A PRO* 3.8 17.6 - - + +
169A CYS* 3.0 6.0 - - - -
170A TYR* 2.8 59.2 + - + +
172A THR* 3.1 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 3.6 9.2 - - + +
79A HIS* 1.3 89.5 - - + +
81A THR* 1.3 62.2 + - - +
84A ALA* 4.5 6.7 - - + -
118A ILE* 4.0 13.0 - - + -
123A ASN 3.9 14.8 - - - +
124A SER* 3.9 33.9 - - - +
125A VAL 4.6 0.7 - - - +
127A PRO* 4.1 17.7 - - + -
128A ILE* 5.1 4.7 - - + -
168A THR 3.6 7.2 - - - +
169A CYS* 3.9 2.7 - - + -
----------------------------------------------------------
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