Contacts of the strand formed by residues 133 - 141 (chain H) in PDB entry 5DSV
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 CYS 133 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30H VAL* 3.8 5.4 - - - -
78H ALA 3.4 14.4 - - - +
80H LEU 3.9 13.0 - - - +
83H ASP* 4.1 5.8 - - - -
84H ALA* 3.5 29.4 - - + -
87H LEU* 3.3 33.3 - - - +
119H VAL* 5.5 1.4 - - - +
131H PHE* 3.2 7.3 + - - +
132H GLY* 1.3 80.4 - - - +
134H SER* 1.3 63.2 + - - +
135H PHE* 4.5 6.5 - - - -
151H ILE 4.4 0.5 - - - +
152H ASP 4.2 1.4 - - - -
153H PRO* 3.6 19.9 - - - +
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Residues in contact with SER 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H VAL* 3.4 19.5 - - - +
77H VAL* 3.7 0.7 - - - +
78H ALA 3.0 28.1 + - - +
133H CYS* 1.3 76.3 - - - +
135H PHE* 1.3 67.2 + - - +
150H MET* 4.4 1.6 - - - -
151H ILE 3.2 11.0 - - - -
152H ASP* 3.5 10.5 - - - +
153H PRO* 3.5 17.3 - - - +
165H ILE* 3.9 25.7 - - - +
169H ARG* 4.1 7.8 + - - -
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Residues in contact with PHE 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H MET* 3.7 20.9 - - + -
76H ALA 3.1 14.1 - - - +
77H VAL* 3.7 17.0 - - + -
87H LEU* 4.0 26.7 - - + -
115H VAL* 3.5 29.8 - - + -
119H VAL* 4.3 3.1 - - + -
133H CYS* 4.5 4.0 - - - -
134H SER* 1.3 82.2 - - - +
136H MET* 1.3 65.9 + - - +
137H LEU* 4.0 25.8 - - + -
150H MET* 3.3 4.9 - - - +
151H ILE* 2.9 78.5 + - + +
165H ILE* 3.9 2.9 - - - -
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Residues in contact with MET 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H ALA 4.5 0.4 - - - +
37H ILE* 4.2 8.1 - - - -
38H GLY* 4.0 19.7 - - - +
47H PHE* 3.7 22.5 - - + -
74H GLY 3.5 0.5 - - - +
75H MET* 3.2 6.4 - - - +
76H ALA* 2.8 40.7 + - - +
135H PHE* 1.3 78.8 - - - +
137H LEU* 1.3 63.9 + - - +
148H LEU* 4.2 10.8 - - + -
149H TYR 2.9 13.7 - - - +
150H MET* 4.0 13.9 - - + -
151H ILE* 6.3 0.2 - - - -
163H CYS* 3.4 52.0 - - + +
164H ALA* 4.0 1.3 - - - +
165H ILE* 4.0 16.4 - - + -
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Residues in contact with LEU 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H PHE* 3.9 2.5 - - - -
69H VAL* 4.5 4.3 - - + -
73H VAL* 4.3 9.9 - - + -
74H GLY 3.2 5.2 - - - +
75H MET* 3.8 34.8 - - + -
91H ALA* 5.3 3.4 - - + -
108H LEU* 3.5 19.6 - - + +
111H LEU* 4.2 16.6 - - + +
112H ALA* 3.9 35.4 - - + +
115H VAL* 5.4 4.0 - - + -
135H PHE* 4.0 22.9 - - + -
136H MET* 1.3 74.2 - - - +
138H GLY* 1.3 58.2 + - - +
148H LEU* 3.4 3.8 - - - +
149H TYR* 2.8 35.6 + - + +
151H ILE* 4.4 2.9 - - + -
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Residues in contact with GLY 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H VAL* 4.6 4.3 - - - -
47H PHE* 3.5 19.0 - - - -
72H HIS 3.9 0.3 - - - +
73H VAL* 3.4 1.2 - - - -
74H GLY* 2.8 34.1 + - - -
108H LEU* 4.0 2.2 - - - +
137H LEU* 1.3 75.0 - - - +
139H SER* 1.3 62.0 + - - -
147H GLN 3.3 9.2 - - - -
148H LEU* 4.5 2.2 - - - -
216H VAL* 4.1 9.8 - - - +
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Residues in contact with SER 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H VAL* 3.9 2.8 - - - +
72H HIS* 3.1 35.7 - - - -
73H VAL* 4.2 0.2 - - - -
108H LEU* 3.7 30.9 + - - +
138H GLY* 1.3 74.1 - - - -
140H TYR* 1.3 63.6 + - - +
141H SER 4.7 0.9 + - - -
144H ASP* 6.1 0.5 - - - +
145H GLY 3.9 0.5 + - - +
146H ALA* 3.6 2.6 - - - -
147H GLN* 3.0 39.5 + - - +
216H VAL* 3.8 9.1 - - - +
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Residues in contact with TYR 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H LYS 4.7 3.1 - - - -
43H ASP* 3.6 24.2 - - - -
44H GLY* 4.4 1.6 - - - -
72H HIS* 4.0 8.3 + - - +
139H SER* 1.3 77.8 - - - +
141H SER* 1.3 83.6 + - - +
142H VAL* 3.9 23.9 - - + +
145H GLY* 3.5 14.6 - - - -
146H ALA* 3.5 22.7 - - + -
216H VAL* 3.7 8.4 - - + +
217H GLY* 3.5 22.9 - - - +
218H GLU* 3.2 44.6 + - + +
221H ASN 5.9 0.4 - - - -
222H GLY* 3.4 28.4 - - - +
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Residues in contact with SER 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H HIS* 5.7 4.9 - - - -
105H ASN* 5.7 6.7 - - - -
139H SER* 4.7 1.8 + - - -
140H TYR* 1.3 87.1 - - - +
142H VAL* 1.3 60.6 + - - +
143H ASN* 3.8 5.3 + - - +
144H ASP* 3.5 28.5 + - - +
145H GLY* 2.9 30.6 + - - +
222H GLY* 5.2 2.7 - - - -
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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