Contacts of the strand formed by residues 134 - 142 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31R ILE* 3.7 7.9 - - - +
78R MET* 3.8 14.4 - - + -
79R SER* 3.4 23.3 - - - +
80R GLY 4.3 0.4 - - - +
81R LEU 3.6 13.7 - - - +
82R THR* 4.6 0.2 - - - -
84R ASP* 3.9 20.2 - - + -
85R ALA* 4.1 13.2 - - + +
88R MET* 3.8 30.9 - - - +
132R PHE* 3.3 8.2 + - + +
133R GLY* 1.3 78.8 - - - +
135R ALA* 1.3 73.0 + - - +
136R LEU* 4.7 1.1 - - + -
151R ALA 4.4 1.4 - - - +
152R GLU 4.9 0.2 - - - -
153R PRO* 3.4 15.8 - - - +
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Residues in contact with ALA 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31R ILE* 3.5 29.0 - - + +
78R MET* 3.4 4.3 - - - -
79R SER 3.0 29.3 + - - -
134R VAL* 1.3 78.0 - - - +
136R LEU* 1.3 61.0 + - - +
150R HIS* 3.6 24.7 - - - +
151R ALA 3.5 6.7 - - - +
152R GLU* 4.9 0.7 - - + -
153R PRO* 4.7 2.2 - - + -
165R ILE* 3.9 12.5 - - + +
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Residues in contact with LEU 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R CYS* 3.9 18.4 - - - -
77R ALA 3.3 4.7 - - - +
78R MET* 3.6 27.6 - - + +
85R ALA* 4.5 13.7 - - + -
88R MET* 3.6 40.6 - - + -
89R ILE* 4.6 4.9 - - + -
116R VAL* 4.0 15.7 - - + -
134R VAL* 4.7 1.3 - - + +
135R ALA* 1.3 77.3 - - - +
137R LEU* 1.3 64.7 + - - +
138R ILE* 3.8 18.3 + - + -
149R PHE 3.4 0.9 - - - +
150R HIS* 3.4 6.5 - - - -
151R ALA* 2.8 41.5 + - + +
165R ILE* 4.5 0.4 - - - -
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Residues in contact with LEU 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37R ALA* 3.6 34.8 - - + +
38R ILE 3.8 2.7 - - - +
39R GLY* 3.7 24.7 - - - +
48R LEU* 4.3 4.9 - - + +
76R CYS* 3.0 8.7 - - - +
77R ALA* 2.7 43.4 + - + +
136R LEU* 1.3 76.3 - - - +
138R ILE* 1.3 59.8 - - - +
139R ALA 3.9 1.0 + - - -
148R LEU* 4.1 12.3 - - + -
149R PHE 3.2 9.0 - - - +
150R HIS* 4.3 4.5 - - + -
163R LYS* 4.0 30.7 - - + +
165R ILE* 3.7 23.5 - - + +
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Residues in contact with ILE 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70R ILE* 4.7 3.6 - - + -
74R ILE* 3.9 24.9 - - + -
75R GLY 3.7 2.5 - - - +
76R CYS* 3.9 12.3 - - + -
109R VAL* 4.3 7.4 - - + -
112R LEU* 4.3 14.8 - - + -
113R THR* 3.6 43.3 - - + +
116R VAL* 4.5 11.9 - - + -
136R LEU* 4.3 21.5 - - + +
137R LEU* 1.3 75.8 - - - +
139R ALA* 1.3 62.1 + - - +
148R LEU* 3.5 2.9 - - - -
149R PHE* 2.8 44.2 + - + +
151R ALA* 4.5 8.3 - - + -
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Residues in contact with ALA 139 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46R VAL* 3.4 33.2 - - + +
48R LEU* 3.6 25.6 - - + -
74R ILE* 3.4 3.4 - - - +
75R GLY 2.9 33.3 + - - +
109R VAL* 4.5 2.9 - - - -
137R LEU 3.9 0.4 + - - -
138R ILE* 1.3 74.7 - - - +
140R GLY* 1.3 58.8 + - - +
147R GLN 3.3 4.9 - - - +
148R LEU* 4.0 2.5 - - + -
215R ILE* 4.2 8.7 - - + +
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Residues in contact with GLY 140 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46R VAL* 4.2 2.6 - - - +
73R HIS 3.0 14.4 - - - -
74R ILE* 4.2 0.7 - - - -
109R VAL* 3.7 18.4 - - - +
139R ALA* 1.3 75.6 - - - +
141R HIS* 1.3 59.9 + - - +
146R TYR* 3.4 4.7 - - - +
147R GLN 2.9 32.1 + - - +
215R ILE* 3.7 11.4 - - - +
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Residues in contact with HIS 141 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73R HIS* 3.1 34.7 + - + +
109R VAL* 3.7 4.7 - - - +
140R GLY* 1.3 74.6 - - - +
142R ASP* 1.3 89.6 + - - +
143R ALA* 4.1 6.0 - - + -
145R GLY* 3.5 27.7 - - - -
146R TYR* 3.5 32.7 - + + -
215R ILE* 3.4 15.7 - - + +
217R LYS* 3.6 41.9 - - + +
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Residues in contact with ASP 142 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73R HIS* 5.0 1.8 - - + -
106R ASP* 6.0 2.7 - - + +
107R ILE 4.8 3.4 - - - +
108R ASN* 3.5 29.8 + - - +
109R VAL* 3.2 22.4 + - + +
141R HIS* 1.3 87.3 + - - +
143R ALA* 1.3 57.4 + - - +
144R ASP* 2.9 31.1 + - - +
145R GLY* 2.8 33.0 + - - -
147R GLN* 3.1 21.3 + - - +
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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