Contacts of the strand formed by residues 66 - 80 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ILE* 4.8 10.3 - - + +
62B TYR 3.7 15.0 - - - -
63B THR* 3.0 6.9 + - - +
64B ALA 3.3 0.6 - - - -
65B LEU* 1.3 106.8 - - + +
67B ARG* 1.3 61.1 + - - +
68B HIS 3.8 10.1 - - - +
69B ALA* 5.7 0.2 - - + -
142B LYS* 3.0 29.4 + - - +
179B LEU* 3.9 36.8 - - + -
180B SER* 3.3 31.6 - - - +
181B SER 3.4 2.7 - - - -
182B PRO* 4.0 18.2 - - + -
183B LEU* 3.6 7.3 - - - +
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Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PRO* 4.6 2.9 - - + -
99A ASN* 5.3 1.3 - - - +
135A THR 3.3 18.2 + - - -
136A ASN 3.5 20.4 + - - -
137A LEU 3.9 1.2 + - - +
138A ASN* 3.7 22.9 - - - +
139A PRO* 5.6 0.2 - - - +
149A ASP* 2.8 40.9 + - + +
66B TYR* 1.3 76.4 - - - +
68B HIS* 1.3 58.9 + - - +
142B LYS* 3.7 6.4 - - - +
143B ALA* 3.3 29.1 + - - +
144B SER* 4.2 4.4 + - - +
181B SER* 2.7 19.8 + - - +
182B PRO 3.7 16.8 - - - -
183B LEU* 3.7 24.0 - - + +
14C ASN* 3.0 20.4 + - - +
15C THR* 3.9 7.7 - - - +
16C LYS 4.5 12.3 + - - +
17C PRO* 4.5 12.9 - - - +
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Residues in contact with HIS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TYR* 3.5 5.3 - - - +
67B ARG* 1.3 79.8 - - - +
69B ALA* 1.3 64.2 + - - +
70B GLN* 3.8 30.6 + - + +
140B ILE* 4.1 14.3 - - + +
142B LYS 3.3 10.8 - - - -
143B ALA* 4.0 3.8 - - + -
178B GLU 4.4 1.8 + - - -
179B LEU* 3.7 2.3 - - - -
180B SER* 3.1 47.7 + - - +
16C LYS* 3.5 35.4 - - + +
17C PRO 3.2 24.2 + - - -
18C SER* 4.0 14.0 - - - -
19C LEU 4.9 1.8 + - - -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 3.7 28.0 - - + -
66B TYR* 5.7 0.4 - - + -
68B HIS* 1.3 78.0 - - - +
70B GLN* 1.3 60.3 + - - +
140B ILE* 3.6 2.8 - - - +
141B ILE* 3.1 26.7 + - + +
142B LYS* 2.9 30.6 + - + +
177B ILE* 3.9 9.0 - - + -
178B GLU 3.3 5.8 - - - -
179B LEU* 4.0 6.5 - - + -
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B HIS* 3.8 22.7 - - + +
69B ALA* 1.3 75.2 - - - +
71B LEU* 1.3 71.6 + - - +
72B LYS 3.5 0.2 + - - -
139B PRO* 3.4 17.7 - - + +
140B ILE* 3.9 20.6 - - + +
177B ILE* 3.9 4.2 - - - +
178B GLU* 2.8 58.9 + - + +
21C PRO* 4.4 18.8 - - - +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 4.2 30.3 - - + -
53B ILE* 4.4 4.0 - - + -
59B LEU* 4.8 4.5 - - + -
70B GLN* 1.3 79.5 + - - +
72B LYS* 1.3 61.0 + - - +
73B HIS 4.5 5.8 - - - +
74B LEU* 4.0 17.9 - - + -
134B LEU* 3.8 20.0 - - + +
139B PRO* 2.9 30.0 + - + +
141B ILE* 3.7 31.2 - - + +
151B PRO* 4.0 23.1 - - + -
176B GLN 3.8 5.2 - - - +
177B ILE* 4.3 13.7 - - + +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B SER* 4.3 14.2 + - - +
70B GLN 3.5 1.0 + - - -
71B LEU* 1.3 73.9 - - - +
73B HIS* 1.3 98.5 + - + +
134B LEU* 3.9 8.0 - - - +
176B GLN* 2.9 34.7 + - + +
178B GLU* 3.9 28.7 - - + +
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Residues in contact with HIS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 3.6 3.8 - - - +
72B LYS* 1.3 121.4 + - + +
74B LEU* 1.3 64.4 + - - +
134B LEU* 4.0 7.0 - - - -
175B GLY* 3.2 20.9 - - - -
176B GLN* 3.4 28.4 + - + +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 4.1 20.6 - - + -
53B ILE* 4.1 13.7 - - + -
71B LEU* 4.0 25.1 - - + -
73B HIS* 1.3 77.5 - - - +
75B LYS* 1.3 69.6 + - - +
95B TRP* 3.7 30.5 - - + -
131B GLU* 3.8 6.2 - - - +
132B ALA* 2.9 37.4 + - + +
134B LEU* 4.2 11.9 - - + +
151B PRO* 4.3 6.1 - - + -
173B ILE* 4.2 22.7 - - + -
174B GLN 3.4 11.0 - - - +
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Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 4.5 7.0 - - - +
74B LEU* 1.3 79.3 - - - +
76B ALA* 1.3 60.8 + - - +
77B THR* 4.0 9.4 - - - +
95B TRP* 4.0 6.7 - - - -
129B ASP* 2.9 39.6 + - + +
130B VAL 3.5 13.5 - - - +
131B GLU* 3.8 18.8 - - + +
132B ALA 4.2 1.1 - - - +
173B ILE* 3.2 5.7 - - - +
174B GLN* 2.9 66.6 + - - +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LYS* 1.3 74.9 - - - +
77B THR* 1.3 67.3 + - - +
78B ILE* 5.8 0.4 - - - -
93B LEU* 4.5 11.9 - - + -
95B TRP* 3.8 19.8 - - + +
129B ASP* 3.5 1.0 - - - -
130B VAL* 2.9 38.7 + - + +
153B LEU* 4.5 8.3 - - + -
171B LEU* 4.3 13.7 - - + -
172B THR 3.2 9.0 - - - +
173B ILE* 4.3 5.4 - - + -
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LYS* 4.3 11.7 + - - +
75B LYS* 4.0 12.6 + - - +
76B ALA* 1.3 76.0 + - - +
78B ILE* 1.3 73.7 + - - +
79B HIS* 3.5 31.3 - - + +
127B PRO* 4.5 2.5 - - + -
128B ILE 3.2 9.2 - - - +
129B ASP* 2.7 27.1 + - - +
170B TYR 3.4 1.9 - - - +
171B LEU* 3.4 4.4 - - - -
172B THR* 2.8 40.3 + - - -
174B GLN* 5.6 2.8 - - - +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 6.0 0.7 - - + -
76B ALA 5.8 0.2 - - - -
77B THR* 1.3 77.4 - - - +
79B HIS* 1.3 62.6 + - - +
80B PRO* 3.3 4.1 - - + +
91B VAL* 3.9 22.4 - - + -
93B LEU* 4.2 8.7 - - + -
116B PHE* 3.9 33.9 - - + -
118B ILE* 4.1 21.8 - - + -
127B PRO* 3.3 8.0 - - - +
128B ILE* 2.9 40.5 + - + +
130B VAL* 5.6 1.3 - - + -
169B CYS* 4.0 25.6 - - + -
170B TYR 3.4 4.7 - - - +
171B LEU* 4.1 16.2 - - + -
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Residues in contact with HIS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LYS* 5.8 1.6 - - - -
36B GLN* 4.7 12.8 - - - -
77B THR* 3.5 27.0 - - + +
78B ILE* 1.3 74.9 - - - +
80B PRO* 1.3 70.5 - - + +
81B THR* 3.9 3.6 - - - +
127B PRO* 4.5 10.2 - - + +
169B CYS* 3.2 3.7 - - - -
170B TYR* 2.8 52.5 + - + +
172B THR* 2.8 35.7 + - + +
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Residues in contact with PRO 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 3.3 12.1 - - + +
79B HIS* 1.3 90.8 - - - +
81B THR* 1.3 59.3 + - - +
84B ALA* 4.1 10.3 - - + -
118B ILE* 4.0 25.6 - - + -
124B SER 5.2 0.4 - - - +
125B VAL* 3.4 36.6 - - + +
126B LYS 3.7 8.3 - - - +
127B PRO* 3.7 15.0 - - + -
128B ILE* 6.2 0.2 - - + -
168B THR 3.5 7.9 - - - +
169B CYS* 3.8 4.0 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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