Contacts of the strand formed by residues 134 - 142 (chain D) in PDB entry 3TDD
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 VAL 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D ILE* 3.6 7.5 - - - +
78D MET* 3.9 13.2 - - + -
79D SER 3.2 29.6 - - - +
80D GLY 4.2 0.7 - - - +
81D LEU 3.4 15.5 - - - +
82D THR* 4.6 1.6 - - - -
84D ASP* 4.0 6.1 - - + -
85D ALA* 3.9 22.2 - - + +
88D MET* 3.8 31.4 - - - +
132D PHE* 3.3 7.6 + - + +
133D GLY* 1.3 79.6 - - - +
135D ALA* 1.3 68.8 + - - +
136D LEU* 4.5 2.0 - - + -
151D ALA 4.7 1.0 - - - +
152D GLU 5.1 0.2 - - - -
153D PRO* 3.8 12.6 - - - +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ILE* 3.6 27.7 - - + +
78D MET* 3.4 0.3 - - - -
79D SER 3.0 29.7 + - - -
134D VAL* 1.3 75.8 - - - +
136D LEU* 1.3 69.6 + - - +
150D HIS* 3.8 22.9 - - - +
151D ALA 3.5 8.5 - - - +
152D GLU* 4.9 2.9 - - + -
153D PRO* 4.9 0.2 - - - -
165D ILE* 3.8 12.7 - - + +
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ILE* 6.4 0.7 - - + -
76D CYS* 3.8 22.7 - - - -
77D ALA 3.3 5.6 - - - +
78D MET* 3.5 25.1 - - + -
85D ALA* 4.4 12.3 - - + -
88D MET* 4.0 42.0 - - + -
89D ILE* 4.8 5.4 - - + -
116D VAL* 4.4 12.1 - - + -
134D VAL* 4.5 1.8 - - + +
135D ALA* 1.3 83.7 - - - +
137D LEU* 1.3 63.9 + - - +
138D ILE* 3.8 12.1 + - + -
149D PHE 3.5 0.3 - - - +
150D HIS* 3.3 6.4 - - - -
151D ALA* 2.7 42.9 + - + +
165D ILE* 4.5 1.3 - - - -
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ALA* 3.8 33.4 - - + +
38D ILE 3.9 1.8 - - - -
39D GLY* 3.8 22.2 - - - +
48D LEU* 4.0 4.8 - - + +
76D CYS* 3.2 4.7 - - - -
77D ALA* 2.8 39.7 + - + +
136D LEU* 1.3 74.1 - - - +
138D ILE* 1.3 62.6 + - - +
139D ALA 3.8 0.7 + - - -
148D LEU* 4.4 12.8 - - + -
149D PHE 3.0 16.2 - - - +
150D HIS* 4.1 11.4 - - + -
163D LYS* 3.8 33.7 - - + +
165D ILE* 3.8 16.6 - - + -
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Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ILE* 4.7 3.6 - - + -
74D ILE* 3.7 25.8 - - + -
75D GLY 3.8 4.0 - - - +
76D CYS* 4.0 12.1 - - + -
109D VAL* 4.6 7.1 - - + +
112D LEU* 4.2 13.2 - - + -
113D THR* 3.4 46.2 - - + +
116D VAL* 4.5 13.2 - - + -
136D LEU* 4.4 13.0 - - + +
137D LEU* 1.3 74.5 - - - +
139D ALA* 1.3 60.4 + - - +
140D GLY 4.4 0.2 + - - -
147D GLN 3.9 0.7 - - - +
148D LEU* 3.5 1.8 - - - -
149D PHE* 2.7 43.6 + - + +
151D ALA* 4.3 14.6 - - + -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D VAL* 3.5 32.3 - - + -
48D LEU* 3.8 26.0 - - + -
74D ILE* 3.4 5.0 - - - +
75D GLY 2.8 36.8 + - - +
109D VAL* 4.7 0.9 - - - -
137D LEU 3.8 1.0 + - - -
138D ILE* 1.3 75.0 - - - +
140D GLY* 1.3 58.4 + - - +
147D GLN 3.3 4.5 - - - +
148D LEU* 3.9 2.9 - - + -
215D ILE* 4.0 10.8 - - + +
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Residues in contact with GLY 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D VAL* 4.3 2.1 - - - +
73D HIS 3.0 14.1 - - - -
74D ILE* 4.1 1.6 - - - -
109D VAL* 3.5 17.3 - - - +
139D ALA* 1.3 76.4 - - - +
141D HIS* 1.3 59.8 + - - -
146D TYR* 3.3 5.2 - - - +
147D GLN 2.8 31.5 + - - +
215D ILE* 3.9 11.1 - - - +
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Residues in contact with HIS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D HIS* 3.0 36.9 + - + +
109D VAL* 3.4 4.7 - - - +
140D GLY* 1.3 75.7 - - - +
142D ASP* 1.3 82.4 + - - +
143D ALA* 4.3 4.2 - - - -
145D GLY* 3.4 32.6 - - - -
146D TYR* 3.5 37.5 - + + -
215D ILE* 4.4 11.2 - - + -
217D LYS* 3.6 44.7 - - + +
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Residues in contact with ASP 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASP* 2.7 25.7 + - - +
73D HIS* 4.9 1.8 - - + -
106D ASP* 6.0 3.4 - - + -
107D ILE 4.8 2.7 - - - +
108D ASN* 3.7 35.4 + - - +
109D VAL* 3.3 17.0 + - + +
141D HIS* 1.3 89.5 + - - +
143D ALA* 1.3 58.0 + - - +
144D ASP* 2.9 5.0 + - - -
145D GLY* 3.0 24.0 + - - -
147D GLN* 3.0 23.3 + - - +
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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