Contacts of the strand formed by residues 135 - 142 (chain U) 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 ILE 135 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28U PHE* 4.4 19.1 - - + -
31U THR* 3.7 25.4 - - + +
77U VAL 3.7 1.2 - - - +
78U VAL* 3.5 5.4 - - - -
79U ASN* 3.0 32.0 + - - +
134U VAL* 1.3 78.9 - - - +
136U LEU* 1.3 64.0 + - - +
137U THR* 4.7 1.2 + - - +
150U LYS* 3.5 35.9 - - + -
151U THR 3.4 7.2 - - - +
152U ASP* 4.3 4.9 - - + -
153U PRO* 4.2 8.7 - - + -
165U THR* 3.9 26.7 - - + -
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Residues in contact with LEU 136 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76U MET* 3.8 8.5 - - - -
77U VAL 3.8 1.8 - - - -
78U VAL* 3.5 29.4 - - + -
88U ALA* 4.0 25.4 - - + -
116U MET* 4.4 15.0 - - + -
120U SER* 5.8 3.8 - - - +
132U LEU* 6.4 0.4 - - + -
134U VAL* 4.0 16.6 - - + +
135U ILE* 1.3 78.3 - - - +
137U THR* 1.3 61.5 + - - +
138U PHE* 3.6 28.8 - - + -
149U TYR 3.7 0.7 - - - +
150U LYS* 3.0 7.4 - - - +
151U THR* 2.8 54.1 + - - +
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Residues in contact with THR 137 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37U SER* 5.0 1.0 + - - -
38U LEU 6.2 0.4 - - - -
39U ALA* 4.3 10.3 - - + -
75U GLY 3.8 0.3 - - - +
76U MET* 3.3 4.6 - - - +
77U VAL* 3.0 53.4 + - + +
79U ASN* 4.9 2.9 + - - -
135U ILE* 4.7 2.6 + - - +
136U LEU* 1.3 72.3 - - - +
138U PHE* 1.3 62.7 + - - +
139U VAL* 4.1 6.4 + - + +
148U ILE* 3.8 27.1 - - + -
149U TYR 3.6 3.1 - - - +
150U LYS* 3.3 21.9 - - + +
163U THR* 4.2 12.9 - - + +
165U THR* 4.1 5.5 + - - -
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Residues in contact with PHE 138 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70U ILE* 4.6 0.9 - - + -
74U ILE* 4.1 7.6 - - + -
75U GLY 3.4 1.8 - - - +
76U MET* 3.3 43.5 - - + -
92U ALA* 4.5 5.2 - - + -
109U CYS* 3.6 23.1 - - - +
112U LEU* 4.0 25.6 - - + -
113U ALA* 3.9 26.2 - - + -
116U MET* 3.9 21.5 - - + -
136U LEU* 3.6 25.4 - - + -
137U THR* 1.3 70.8 - - - +
139U VAL* 1.3 67.8 + - - +
147U SER 3.5 0.5 - - - +
148U ILE* 3.2 2.1 - - - +
149U TYR* 2.7 44.3 + - + +
151U THR* 4.3 7.9 - - + -
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Residues in contact with VAL 139 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39U ALA* 4.3 0.9 - - + -
46U THR* 3.5 26.2 - - + +
48U VAL* 3.4 35.4 - - + -
73U THR 3.8 0.2 - - - +
74U ILE* 3.5 1.9 - - - +
75U GLY 2.9 42.7 + - - +
76U MET* 5.5 0.2 - - - -
109U CYS* 4.0 2.2 - - - -
137U THR* 4.4 4.0 - - + +
138U PHE* 1.3 81.6 - - - +
140U SER* 1.3 66.4 + - - +
147U SER 3.1 6.5 - - - +
148U ILE* 4.0 14.6 - - + -
215U ALA* 4.5 3.6 - - + +
221U PHE* 3.8 22.7 - - + -
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Residues in contact with SER 140 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46U THR* 3.1 5.9 + - - -
73U THR* 3.1 23.1 - - - -
74U ILE* 4.2 3.8 - - - -
109U CYS* 3.0 28.7 + - - +
139U VAL* 1.3 79.2 - - - +
141U VAL* 1.3 62.6 + - - +
142U ASP* 3.6 10.6 + - - -
147U SER* 2.7 32.1 + - - -
215U ALA* 3.6 16.0 - - - +
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Residues in contact with VAL 141 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U ASP* 4.2 11.0 - - + +
45U CYS* 3.8 16.4 - - - +
46U THR* 4.4 0.4 - - - +
73U THR* 4.6 7.4 + - - +
140U SER* 1.3 79.0 - - - +
142U ASP* 1.3 64.3 + - - +
143U GLU 3.5 1.6 + - - -
145U GLY* 3.8 8.3 - - - -
146U PRO* 4.0 16.8 - - + -
215U ALA* 3.2 29.3 - - - +
216U THR* 3.3 25.4 + - - +
217U LYS* 3.7 30.6 + - + +
218U ASP 5.0 1.4 + - - -
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Residues in contact with ASP 142 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14U GLU* 2.9 10.4 + - - +
108U PRO* 3.5 21.2 - - - +
109U CYS* 4.4 2.5 + - + +
110U ASP* 4.8 1.1 - - - +
140U SER* 3.6 11.0 + - - +
141U VAL* 1.3 75.6 - - - +
143U GLU* 1.3 67.9 + - - +
144U LEU* 2.7 31.0 + - + +
145U GLY* 2.8 39.6 + - - +
147U SER* 4.0 6.3 - - - +
217U LYS* 3.7 4.0 + - - -
72V ARG* 3.1 30.0 + - - -
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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