Contacts of the strand formed by residues 134 - 142 (chain F) in PDB entry 3SDI
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31F VAL* 3.5 7.1 - - - +
78F TYR* 4.4 8.5 - - + -
79F SER 3.4 12.6 - - - +
80F GLY 4.0 1.1 - - - -
81F LEU 3.0 36.1 - - - +
84F ASP* 4.1 8.3 - - + +
85F GLY* 3.8 26.5 - - - +
88F LEU* 4.7 7.6 - - + -
132F PHE* 3.3 13.2 + - + +
133F GLY* 1.3 82.2 - - - +
135F SER* 1.3 64.0 - - - +
136F THR* 4.3 12.7 + - - +
151F LEU 4.2 1.4 - - - +
152F GLU 4.3 0.5 - - - -
153F PRO* 3.4 23.4 - - - +
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Residues in contact with SER 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F VAL* 3.6 9.8 - - - +
78F TYR* 3.0 5.6 - - - +
79F SER 3.0 30.1 + - - -
134F VAL* 1.3 73.4 - - - +
136F THR* 1.3 60.4 + - - +
150F MET* 5.0 4.0 - - - -
151F LEU 3.2 9.3 + - - -
152F GLU* 2.5 33.2 + - - -
153F PRO* 4.0 4.2 - - - +
165F THR* 3.4 30.4 + - - +
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Residues in contact with THR 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F CYS* 4.2 17.5 - - + -
77F VAL 3.2 15.0 - - - +
78F TYR* 3.9 20.9 - - + +
88F LEU* 3.5 28.7 - - + +
89F VAL* 5.5 2.7 - - + -
116F LEU* 5.3 2.9 - - + -
134F VAL* 4.3 5.5 - - - +
135F SER* 1.3 76.3 - - - +
137F ILE* 1.3 62.4 + - - +
138F PHE* 3.8 15.7 - - + -
149F TYR 3.7 0.7 - - - +
150F MET* 3.3 4.9 - - - +
151F LEU* 3.0 39.0 + - - +
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Residues in contact with ILE 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F SER* 3.5 32.5 - - - +
38F ILE* 3.9 3.4 - - - -
39F GLY* 3.8 15.5 - - - +
48F PHE* 4.0 8.4 - - + -
76F CYS* 3.5 0.3 - - - -
77F VAL* 2.6 48.1 + - + +
135F SER 4.4 0.2 + - - -
136F THR* 1.3 74.0 - - - +
138F PHE* 1.3 62.3 + - - +
148F LEU* 3.7 24.7 - - + -
149F TYR 3.3 5.4 - - - +
150F MET* 3.8 18.8 - - + -
163F ALA* 4.0 6.5 - - + +
164F ALA* 3.9 18.2 - - - +
165F THR* 3.7 19.1 - - + -
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Residues in contact with PHE 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F PHE* 3.6 8.5 - - - -
74F ILE* 4.7 0.7 - - + -
75F GLY 3.1 14.8 - - - +
76F CYS* 3.6 16.6 - - + -
109F ILE* 4.6 2.5 - - + -
112F PHE* 3.7 26.0 - + - -
113F ALA* 3.6 36.8 - - + -
116F LEU* 4.0 20.6 - - + -
136F THR* 3.8 16.4 - - - -
137F ILE* 1.3 75.0 - - - +
139F GLY* 1.3 61.9 + - - +
148F LEU* 3.5 2.3 - - - +
149F TYR* 2.7 69.1 + + + -
151F LEU* 4.0 23.1 - - + -
157F TYR* 5.4 2.7 - - + -
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Residues in contact with GLY 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F VAL* 4.0 0.6 - - - +
48F PHE* 3.3 14.7 - - - -
74F ILE* 3.5 9.0 - - - +
75F GLY 3.0 28.0 + - - -
109F ILE* 3.7 14.8 - - - -
138F PHE* 1.3 80.0 - - - +
140F GLY* 1.3 56.5 + - - -
147F HIS 3.1 14.1 - - - -
215F CYS* 5.2 0.3 - - - +
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Residues in contact with GLY 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F VAL* 3.8 14.5 - - - +
73F HIS 3.3 15.3 - - - -
109F ILE* 3.6 16.3 - - - +
139F GLY* 1.3 75.0 - - - -
141F VAL* 1.3 64.0 + - - -
145F GLY 3.9 0.2 - - - +
146F ALA* 3.5 1.5 - - - +
147F HIS 3.0 30.0 + - - -
215F CYS* 4.0 3.6 - - - -
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Residues in contact with VAL 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F ASP 3.7 22.2 - - - +
45F GLY* 4.2 4.7 - - - -
73F HIS* 3.4 26.3 + - - +
109F ILE* 4.4 0.9 - - - -
140F GLY* 1.3 75.8 - - - +
142F ASP* 1.3 75.5 + - - +
145F GLY* 3.4 9.6 - - - +
146F ALA* 4.5 4.7 - - - +
215F CYS* 3.7 30.2 - - - +
217F LEU* 4.2 32.3 - - + +
219F GLY* 4.3 10.7 - - - +
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Residues in contact with ASP 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F HIS* 5.0 2.2 - - + -
106F PRO 5.8 1.3 - - - +
107F ILE 5.0 1.3 - - - +
108F PRO* 3.5 26.5 - - + +
109F ILE* 3.2 24.2 + - + -
110F PRO* 3.5 2.9 - - - +
140F GLY 4.2 0.2 + - - -
141F VAL* 1.3 86.2 - - - +
143F LYS* 1.3 57.8 + - + +
144F ASN* 2.8 35.8 + - - +
145F GLY 3.0 17.2 + - - +
147F HIS* 3.1 25.0 - - - -
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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