Contacts of the strand formed by residues 169 - 182 (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 CYS 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A SER* 3.7 2.8 - - - -
42A LEU* 2.8 46.7 + - - +
78A ILE* 4.0 22.0 - - + -
79A HIS 3.0 20.4 - - - +
80A PRO* 3.9 2.7 - - + -
81A THR* 3.8 5.1 - - - +
89A THR* 4.9 1.3 - - - -
91A VAL* 4.1 16.2 - - - -
118A ILE* 4.0 11.2 - - + -
167A PRO* 3.3 3.3 - - - +
168A THR* 1.3 93.2 + - - +
170A TYR* 1.3 65.2 + - - +
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Residues in contact with TYR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 4.7 13.0 - - + -
40A ALA 3.4 4.3 - - - +
41A SER* 4.0 22.2 - - - -
42A LEU* 5.3 0.2 - - - -
77A THR 3.5 1.6 - - - +
78A ILE* 3.4 6.9 - - - +
79A HIS* 2.8 49.1 + - + +
81A THR* 3.6 27.4 - - + +
167A PRO* 3.7 27.7 - - + +
169A CYS* 1.3 74.3 - - - +
171A LEU* 1.3 62.5 + - - +
172A THR* 4.9 5.6 - - + -
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 3.8 0.9 - - - +
39A LEU* 2.8 35.6 + - + -
40A ALA* 2.9 19.1 + - + +
42A LEU* 4.2 17.0 - - + +
76A ALA* 4.3 7.6 - - + -
77A THR 3.4 15.5 - - - +
78A ILE* 4.3 7.9 - - + +
91A VAL* 5.9 0.9 - - + -
93A LEU* 3.8 23.3 - - + -
153A LEU* 4.3 10.5 - - + -
155A TYR* 3.8 46.0 - - + -
170A TYR* 1.3 75.3 - - - +
172A THR* 1.3 69.6 + - - +
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Residues in contact with THR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLN* 2.9 27.5 + - + +
37A ILE 3.2 16.8 - - - +
38A THR* 4.0 19.1 - - + +
39A LEU* 4.1 2.0 - - - +
76A ALA* 3.3 6.2 - - - +
77A THR* 2.9 35.2 + - - +
79A HIS* 3.1 27.8 + - + +
170A TYR* 4.9 3.6 - - + -
171A LEU* 1.3 82.3 - - - +
173A ILE* 1.3 67.2 + - - +
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Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 4.3 15.8 - - + -
36A GLN* 3.3 3.6 - - - +
37A ILE* 2.8 57.0 + - + +
39A LEU* 3.7 29.6 - - + -
53A ILE* 3.8 27.1 - - + -
56A ASN* 5.6 4.5 - - - -
59A LEU* 5.4 2.9 - - + -
74A LEU* 4.4 7.6 - - + -
75A LYS 3.2 12.3 - - - +
76A ALA* 4.4 4.5 - - + -
95A TRP* 3.9 23.8 - - + -
153A LEU* 4.6 0.9 - - + -
172A THR* 1.3 79.7 - - - +
174A GLN* 1.3 61.3 + - - +
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.3 19.5 - - - +
36A GLN* 3.3 32.5 + - + +
74A LEU* 3.4 3.0 - - - +
75A LYS* 2.9 67.9 + - + +
77A THR* 5.2 2.7 + - - +
172A THR* 5.3 0.2 - - - +
173A ILE* 1.3 76.2 - - - +
175A GLY* 1.3 65.5 + - - +
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PRO* 3.4 3.8 - - - +
35A PHE* 3.0 45.8 + - - +
73A HIS* 3.2 17.9 - - - -
174A GLN* 1.3 81.3 - - - +
176A GLN* 1.3 65.9 + - - +
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Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER* 4.0 20.0 - - - +
33A TYR 3.4 7.2 - - - +
34A PRO* 4.3 16.9 - - + +
35A PHE* 3.8 2.2 - - - -
71A LEU* 3.7 3.6 - - - +
72A LYS* 2.9 50.6 + - + +
73A HIS* 3.1 32.1 + - + +
175A GLY* 1.3 80.8 - - - +
177A ILE* 1.3 61.8 + - - +
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Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE 3.6 0.2 - - - +
32A SER* 3.4 2.0 - - - -
33A TYR* 2.9 45.1 + - + +
35A PHE* 4.1 17.0 - - + -
59A LEU* 4.4 12.3 - - + -
62A TYR* 5.1 7.0 - - + -
63A THR* 3.7 29.2 - - + -
69A ALA* 3.7 9.4 - - + -
70A GLN 3.6 13.7 - - - +
71A LEU* 4.4 6.3 - - + +
141A ILE* 3.7 18.4 - - + -
176A GLN* 1.3 75.6 - - - +
178A GLU* 1.3 72.7 + - - +
179A LEU* 3.6 17.5 + - + +
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A VAL* 3.7 24.8 - - + +
31A ILE 3.3 5.2 - - - -
32A SER* 4.2 10.3 - - - +
68A HIS* 3.7 3.0 + - - +
69A ALA* 3.3 5.5 - - - -
70A GLN* 2.7 65.5 + - + +
72A LYS* 3.8 38.7 - - + +
177A ILE* 1.3 71.2 - - - +
179A LEU* 1.3 58.9 + - - +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PRO 4.0 0.3 - - - +
30A VAL* 3.5 2.0 - - - -
31A ILE* 2.8 44.3 + - + +
33A TYR* 4.3 23.1 - - + -
62A TYR* 4.1 13.0 - - + +
63A THR* 4.2 14.8 - - + -
66A TYR* 3.8 40.7 - - + +
68A HIS 3.5 3.4 - - - +
69A ALA* 4.0 20.4 - - + -
177A ILE* 3.9 20.0 - - + +
178A GLU* 1.3 80.6 - - - +
180A SER* 1.3 63.9 + - - +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 4.7 7.0 - - - +
29A PRO 3.3 20.2 - - - -
30A VAL* 3.8 16.7 - - - +
66A TYR* 3.4 12.1 - - - +
68A HIS* 3.2 43.4 + - - +
179A LEU* 1.3 77.7 - - - +
181A SER* 1.3 76.9 + - - +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 3.3 22.9 - - - +
29A PRO 4.6 1.0 + - - -
66A TYR* 3.5 0.6 - - - -
67A ARG* 2.7 41.0 + - - +
68A HIS* 4.6 4.2 - - - +
180A SER* 1.3 76.1 + - - +
182A PRO* 1.3 75.5 - - - +
15B THR* 3.5 13.0 - - - +
16B LYS 3.2 28.8 + - - -
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Residues in contact with PRO 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 5.5 1.3 - - + -
29A PRO* 6.5 0.4 - - + -
65A LEU 3.5 9.4 - - - +
66A TYR* 4.0 14.6 - - + -
67A ARG* 3.7 1.4 - - - -
180A SER 4.0 0.2 - - - -
181A SER* 1.3 86.1 - - - +
183A LEU* 1.3 62.4 + - - +
184A LEU* 4.0 3.8 + - + +
13B LEU* 3.7 25.6 - - + +
14B ASN 3.8 16.8 - - - +
15B THR* 2.7 28.1 + - - +
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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