Contacts of the strand formed by residues 145 - 151 (chain S) 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 GLY 145 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43S ASN 5.0 3.4 - - - -
141S TYR* 3.3 24.6 - - - -
142S ASP 3.0 30.6 + - - -
143S LYS 3.6 0.6 - - - -
144S SER* 1.3 79.1 - - - +
146S ALA* 1.3 61.9 + - - -
147S HIS* 3.0 8.7 - - - -
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Residues in contact with ALA 146 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41S ARG* 3.4 27.0 + - + +
42S SER 4.2 7.9 - - - +
43S ASN* 4.5 5.2 + - - +
44S THR 4.5 0.7 - - - -
45S HIS 3.5 37.0 - - - +
46S ALA* 4.4 2.2 - - + -
140S GLY 3.6 5.4 - - - -
141S TYR* 3.3 16.2 - - + -
144S SER 4.7 0.9 - - - +
145S GLY* 1.3 72.6 - - - -
147S HIS* 1.3 71.7 + - - +
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Residues in contact with HIS 147 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41S ARG* 3.6 8.3 - - - +
46S ALA* 3.8 3.7 - - - +
109S VAL* 3.5 25.9 - - + +
110S GLU* 5.5 6.3 + - + +
138S ILE 4.2 0.4 - - - -
139S ILE* 3.1 27.5 - - - +
140S GLY 2.9 14.1 + - - +
142S ASP* 2.8 34.5 + - - -
144S SER* 2.9 25.3 + - - -
145S GLY 3.0 25.6 + - - -
146S ALA* 1.3 80.6 + - - +
148S LEU* 1.3 61.5 + - - +
149S LEU* 4.8 0.4 - - + -
159S GLU* 2.6 29.6 + - - +
63T LYS* 5.2 9.6 - - - -
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Residues in contact with LEU 148 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39S GLY* 3.2 39.5 - - - +
41S ARG* 3.9 11.9 - - + +
137S LEU* 4.5 9.4 - - + -
138S ILE 3.2 4.7 - - - +
139S ILE* 3.5 25.8 - - + -
147S HIS* 1.3 75.7 - - - +
149S LEU* 1.3 85.1 + - - +
159S GLU* 3.3 2.4 - - - +
160S LEU* 2.9 39.9 + - + +
161S TYR 3.8 2.5 - - - +
162S GLY* 3.2 28.7 - - - +
163S THR* 3.8 10.1 - - + +
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Residues in contact with LEU 149 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109S VAL* 3.2 44.4 - - + +
110S GLU* 4.6 5.4 - - - -
113S GLY* 3.6 23.8 - - - +
137S LEU* 3.1 9.1 - - - +
138S ILE* 2.6 54.7 + - + +
148S LEU* 1.3 91.2 - - - +
150S GLU* 1.3 59.9 + - - +
151S PHE 4.1 0.2 - - - -
157S VAL* 3.8 16.6 - - + -
158S THR 3.2 5.4 - - - +
159S GLU* 3.7 26.5 - - + -
160S LEU* 5.5 0.4 - - - -
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Residues in contact with GLU 150 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136S LEU 3.4 2.2 - - - +
137S LEU* 3.5 18.8 - - + -
149S LEU* 1.3 72.7 - - - +
151S PHE* 1.3 61.3 + - - +
152S GLN* 2.9 32.9 + - + +
156S ASN 3.4 3.5 - - - +
157S VAL* 3.1 7.0 - - - -
158S THR* 2.8 37.4 + - - +
160S LEU* 3.6 17.6 - - + +
163S THR* 2.8 28.5 + - - +
165S ILE* 3.7 13.2 - - + +
173S LYS* 4.0 12.6 + - - -
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Residues in contact with PHE 151 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88S LEU* 3.5 31.0 - - + -
116S LEU* 3.7 23.1 - - + -
120S ALA* 3.7 30.3 - - + -
132S TYR* 5.0 1.6 - - + -
134S VAL* 3.6 16.4 - - + -
135S GLY* 3.4 5.7 - - - -
136S LEU* 2.6 64.8 + - + +
138S ILE* 4.1 11.7 - - + -
149S LEU 4.1 0.4 - - - -
150S GLU* 1.3 72.4 - - - +
152S GLN* 1.3 82.2 + - - +
153S PRO* 4.1 6.5 - - + -
155S GLY* 4.4 2.9 - - - -
156S ASN 3.8 1.6 - - - -
157S VAL* 3.7 22.2 - - + -
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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