Contacts of the strand formed by residues 134 - 142 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ILE* 3.4 7.6 - - - +
78B VAL* 4.3 4.9 - - + -
79B ALA 3.6 3.6 - - - -
80B GLY 4.7 0.2 - - - -
81B LEU 3.4 25.1 - - - +
84B ASP* 3.5 10.3 - - + -
85B ALA* 3.4 21.8 - - + +
88B LEU* 4.6 6.5 - - + -
120B LYS* 3.5 13.2 + - - -
132B PHE* 2.8 13.2 + - + +
133B GLY* 1.3 81.3 - - - +
135B SER* 1.3 69.5 + - - +
136B PHE* 3.6 36.3 - - + -
153B PRO* 3.3 17.7 - - - +
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Residues in contact with SER 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 4.5 2.6 - - - +
31B ILE* 3.3 26.1 - - - +
77B ALA 3.8 1.4 - - - +
78B VAL* 3.8 2.1 - - - -
79B ALA* 2.9 35.6 + - - +
134B VAL* 1.3 73.1 - - - +
136B PHE* 1.3 62.1 + - - +
150B THR* 5.8 0.2 - - - -
151B SER 3.2 7.4 - - - -
152B ASN* 3.3 24.8 - - - +
165B VAL* 4.4 20.8 - - - +
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Residues in contact with PHE 136 (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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76B VAL* 3.8 20.9 - - + -
77B ALA 3.4 1.8 - - - -
78B VAL* 3.6 28.5 - - + -
85B ALA 3.9 8.1 - - - -
88B LEU* 3.7 32.8 - - + -
89B ILE* 3.9 16.6 - - + -
116B LEU* 4.6 9.0 - - + -
120B LYS* 3.1 27.8 - - - -
134B VAL* 3.6 22.0 - - + -
135B SER* 1.3 74.6 - - - +
137B ILE* 1.3 64.7 + - - +
138B TYR* 3.7 33.0 - + + -
150B THR* 3.2 10.6 + - - -
151B SER* 2.8 29.6 + - - +
165B VAL* 4.6 0.8 - - - +
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Residues in contact with ILE 137 (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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37B ALA* 3.4 35.9 - - + +
38B ILE 4.0 1.3 - - - -
39B GLY* 3.9 15.5 - - - +
48B LEU* 3.7 20.2 - - + +
76B VAL* 3.1 6.3 - - - +
77B ALA* 2.8 38.2 + - + +
136B PHE* 1.3 73.8 - - - +
138B TYR* 1.3 63.1 + - - +
139B ALA 4.0 0.3 + - - -
148B LEU* 4.0 16.2 - - + -
149B TYR 3.2 9.2 - - - +
150B THR* 4.3 3.1 - - - +
163B ILE* 3.9 15.0 - - + +
164B SER* 4.2 0.2 - - - -
165B VAL* 3.7 34.1 - - + -
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Residues in contact with TYR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.4 5.8 - - + -
74B ILE* 5.1 5.8 - - + -
75B ALA 3.6 4.3 - - - +
76B VAL* 3.3 25.8 - - + -
109B VAL* 5.2 2.0 - - + -
112B LEU* 4.5 4.9 - - + -
113B VAL* 3.4 44.1 + - + -
116B LEU* 3.7 38.2 - - + +
117B SER 4.9 0.3 + - - -
120B LYS* 4.4 0.5 + - - -
136B PHE* 3.7 16.5 - - + -
137B ILE* 1.3 74.3 - - - +
139B ALA* 1.3 62.1 + - - +
140B GLY 4.1 0.2 - - - -
147B GLN 3.5 1.8 - - - +
148B LEU* 3.1 11.8 - - - +
149B TYR* 2.6 54.5 + - + -
151B SER* 2.7 41.3 + - - -
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Residues in contact with ALA 139 (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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46B ILE* 3.6 26.7 - - + -
48B LEU* 3.6 31.4 - - + -
74B ILE* 3.5 1.9 - - - +
75B ALA 2.8 32.9 + - - -
137B ILE 4.0 1.0 + - - -
138B TYR* 1.3 73.2 - - - +
140B GLY* 1.3 58.3 + - - +
147B GLN 3.7 4.7 - - - -
148B LEU* 4.0 2.2 - - + -
215B ILE* 3.1 15.8 - - + +
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Residues in contact with GLY 140 (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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46B ILE* 3.6 6.3 - - - +
73B LYS 3.0 13.0 - - - -
74B ILE* 4.1 4.3 - - - -
109B VAL* 3.7 18.0 - - - +
138B TYR 4.1 0.8 - - - -
139B ALA* 1.3 74.7 - - - +
141B TYR* 1.3 61.3 + - - -
146B TYR* 3.5 3.6 - - - -
147B GLN* 2.8 35.1 + - - +
215B ILE* 3.9 4.0 - - - -
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Residues in contact with TYR 141 (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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21B VAL* 2.8 70.8 + - + -
73B LYS* 3.0 35.4 + - + +
74B ILE* 5.1 0.3 - - - +
107B ILE 5.7 0.3 - - - +
109B VAL* 3.5 7.1 - - - +
140B GLY* 1.3 75.2 - - - +
142B ASP* 1.3 79.7 + - - +
143B ASP* 4.2 10.2 - - + +
145B GLY* 3.2 36.2 - - - -
146B TYR* 3.5 35.2 - + + -
215B ILE* 4.5 0.9 - - + -
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Residues in contact with ASP 142 (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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14B TYR* 2.9 13.9 + - - +
73B LYS* 5.3 2.9 - - + -
106B ASP 5.9 1.1 - - - +
107B ILE 5.0 1.8 - - - +
108B PRO* 3.7 16.2 - - + +
109B VAL* 2.9 27.5 + - + +
110B GLU 4.6 0.5 + - - -
141B TYR* 1.3 86.4 + - - +
143B ASP* 1.3 60.8 + - - +
144B ARG* 2.8 22.5 + - - +
145B GLY* 2.8 31.3 + - - -
147B GLN* 2.6 22.3 + - - +
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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