Contacts of the strand formed by residues 135 - 142 (chain G) 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 ILE 135 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G PHE* 4.6 12.8 - - + -
31G THR* 3.9 23.8 - - + +
77G VAL 3.8 0.9 - - - +
78G VAL* 3.4 4.9 - - - +
79G ASN* 2.9 34.5 + - - +
134G VAL* 1.3 77.7 - - - +
136G LEU* 1.3 62.4 - - - +
137G THR* 4.7 1.8 + - - +
150G LYS* 3.5 37.9 - - + -
151G THR 3.4 7.6 - - - +
152G ASP* 4.1 19.7 - - + -
153G PRO* 4.2 1.1 - - + -
165G THR* 3.8 26.7 - - + -
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Residues in contact with LEU 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G MET* 3.9 14.1 - - - -
77G VAL 3.8 2.2 - - - -
78G VAL* 3.9 15.9 - - + -
88G ALA* 3.7 31.9 - - + -
116G MET* 4.3 18.2 - - + +
120G SER* 5.8 2.9 - - - +
132G LEU* 6.2 0.7 - - + -
134G VAL* 4.0 18.8 - - + +
135G ILE* 1.3 73.8 - - - +
137G THR* 1.3 61.7 + - - +
138G PHE* 3.6 26.3 + - + -
149G TYR 3.8 0.9 - - - +
150G LYS* 3.1 5.7 - - - +
151G THR* 2.8 57.5 + - - +
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Residues in contact with THR 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G SER* 4.8 1.4 + - - -
39G ALA* 4.4 9.0 - - + -
75G GLY 3.8 0.3 - - - +
76G MET* 3.1 5.4 - - - -
77G VAL* 2.8 63.3 + - + +
79G ASN* 4.9 1.0 + - - -
135G ILE* 4.7 2.4 + - - +
136G LEU* 1.3 72.3 - - - +
138G PHE* 1.3 62.3 + - - +
139G VAL* 4.1 5.8 + - + +
148G ILE* 3.7 27.6 - - + -
149G TYR 3.6 3.4 - - - +
150G LYS* 3.4 21.6 - - + +
163G THR* 4.3 12.1 - - + -
165G THR* 3.9 8.3 + - - -
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Residues in contact with PHE 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G ILE* 4.4 3.6 - - + -
74G ILE* 4.0 8.7 - - + -
75G GLY 3.4 0.7 - - - -
76G MET* 3.3 42.2 - - + -
92G ALA* 4.4 2.7 - - + -
109G CYS* 3.5 21.9 - - - +
112G LEU* 3.7 27.8 - - + -
113G ALA* 4.1 23.1 - - + -
116G MET* 3.9 21.8 - - + -
136G LEU* 3.6 24.5 - - + -
137G THR* 1.3 71.4 - - - +
139G VAL* 1.3 64.1 + - - +
148G ILE* 3.3 5.9 - - - +
149G TYR* 2.7 45.3 + - + +
151G THR* 4.1 9.9 - - + -
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Residues in contact with VAL 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G THR* 3.6 28.0 - - + +
48G VAL* 3.5 34.5 - - + -
73G THR 3.8 0.2 - - - +
74G ILE* 3.4 3.5 - - - +
75G GLY 2.9 41.0 + - - +
76G MET* 5.6 0.2 - - - -
109G CYS* 3.8 3.1 - - - -
137G THR* 4.5 3.1 - - + +
138G PHE* 1.3 81.4 - - - +
140G SER* 1.3 65.3 + - - +
147G SER 3.2 6.1 - - - +
148G ILE* 3.8 15.3 - - + -
215G ALA* 4.4 4.1 - - + +
221G PHE* 3.8 26.5 - - + -
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Residues in contact with SER 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G THR* 3.1 6.7 + - - -
73G THR* 3.2 25.8 - - - -
74G ILE* 4.3 5.2 - - - -
109G CYS* 3.2 27.4 + - - +
139G VAL* 1.3 79.3 - - - +
141G VAL* 1.3 62.3 + - - +
142G ASP* 3.7 11.6 + - - -
147G SER* 2.7 34.2 + - - -
215G ALA* 3.7 8.5 - - - +
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Residues in contact with VAL 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G ASP* 3.8 9.0 - - + +
45G CYS* 3.7 20.2 - - - +
73G THR* 4.6 8.0 + - - +
140G SER* 1.3 76.7 - - - +
142G ASP* 1.3 70.1 + - - +
143G GLU* 3.5 2.1 + - - -
145G GLY* 3.9 6.3 - - - -
146G PRO* 3.9 20.2 - - + -
215G ALA* 3.3 27.1 - - - +
216G THR* 3.7 14.4 + - - +
217G LYS* 3.8 35.2 - - + +
218G ASP 5.1 2.3 + - - -
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Residues in contact with ASP 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G PRO* 3.3 21.8 - - - +
109G CYS* 4.5 2.4 + - + -
110G ASP* 4.6 2.2 - - - +
140G SER* 3.7 10.1 + - - +
141G VAL* 1.3 76.8 - - - +
143G GLU* 1.3 74.2 + - - +
144G LEU* 2.7 29.5 + - + +
145G GLY* 2.9 39.2 + - - +
147G SER* 4.1 7.0 - - - +
217G LYS* 5.0 1.8 + - - -
72H ARG* 2.9 32.6 + - - -
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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