Contacts of the strand formed by residues 133 - 141 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30L VAL* 3.8 5.4 - - - -
78L ALA 3.4 14.8 - - - +
80L LEU 3.9 12.6 - - - +
83L ASP* 4.0 5.6 - - - -
84L ALA* 3.5 29.8 - - + +
87L LEU* 3.3 32.6 - - - +
119L VAL* 5.5 1.4 - - - +
131L PHE* 3.2 8.1 + - - +
132L GLY* 1.3 80.5 - - - +
134L SER* 1.3 63.8 + - - +
135L PHE* 4.5 6.2 - - - -
151L ILE 4.4 0.5 - - - +
152L ASP 4.2 1.7 - - - -
153L PRO* 3.6 19.3 - - - +
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Residues in contact with SER 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L VAL* 3.4 19.8 - - - +
77L VAL* 3.7 1.0 - - - +
78L ALA 3.0 27.9 + - - +
133L CYS* 1.3 77.3 - - - +
135L PHE* 1.3 66.8 + - - +
150L MET* 4.4 2.0 - - - -
151L ILE 3.2 11.2 - - - -
152L ASP* 3.5 10.2 - - - +
153L PRO* 3.5 17.7 - - - +
165L ILE* 3.9 24.5 - - - +
169L ARG* 4.0 7.3 + - - -
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Residues in contact with PHE 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L MET* 3.7 26.9 - - + -
76L ALA 3.1 14.4 - - - +
77L VAL* 3.7 17.3 - - + -
87L LEU* 4.0 28.3 - - + -
115L VAL* 3.5 28.3 - - + -
119L VAL* 4.3 2.9 - - + -
133L CYS* 4.5 3.6 - - - -
134L SER* 1.3 82.5 - - - +
136L MET* 1.3 65.8 + - - +
137L LEU* 3.9 21.1 - - + -
150L MET* 3.3 5.1 - - - +
151L ILE* 2.8 77.6 + - + +
165L ILE* 3.9 2.2 - - - -
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Residues in contact with MET 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L ALA 4.5 0.4 - - - +
37L ILE* 4.2 5.4 - - - -
38L GLY* 4.0 20.9 - - - +
47L PHE* 3.8 21.2 - - + -
74L GLY 3.5 0.9 - - - +
75L MET* 3.2 5.9 - - - +
76L ALA* 2.8 41.3 + - - +
135L PHE* 1.3 79.1 - - - +
137L LEU* 1.3 63.4 + - - +
148L LEU* 4.2 10.1 - - + -
149L TYR 2.9 13.9 - - - +
150L MET* 4.0 14.6 - - + -
163L CYS* 3.4 51.4 - - + +
164L ALA* 4.0 1.1 - - - +
165L ILE* 4.0 18.8 - - + -
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Residues in contact with LEU 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L PHE* 3.9 2.2 - - - -
69L VAL* 4.5 4.3 - - + -
73L VAL* 4.3 9.9 - - + -
74L GLY 3.2 4.7 - - - +
75L MET* 3.8 34.3 - - + -
91L ALA* 5.3 3.1 - - + -
108L LEU* 3.5 20.0 - - + +
111L LEU* 4.3 16.6 - - + +
112L ALA* 3.9 35.0 - - + +
115L VAL* 5.4 4.0 - - + -
135L PHE* 3.9 23.1 - - + -
136L MET* 1.3 74.8 - - - +
138L GLY* 1.3 58.9 + - - +
148L LEU* 3.4 3.3 - - - +
149L TYR* 2.8 35.0 + - + +
151L ILE* 4.4 3.4 - - + -
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Residues in contact with GLY 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L VAL* 4.6 4.0 - - - -
47L PHE* 3.6 18.8 - - - -
72L HIS 3.9 0.3 - - - +
73L VAL* 3.4 1.6 - - - -
74L GLY* 2.8 34.4 + - - +
108L LEU* 3.9 2.2 - - - +
137L LEU* 1.3 74.9 - - - +
139L SER* 1.3 62.8 + - - -
147L GLN 3.3 9.4 - - - -
148L LEU* 4.5 2.0 - - - -
216L VAL* 4.1 10.3 - - - +
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Residues in contact with SER 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L VAL* 3.9 2.4 - - - +
72L HIS* 3.1 36.2 - - - -
73L VAL* 4.2 0.2 - - - -
108L LEU* 3.6 31.7 + - - +
138L GLY* 1.3 73.2 - - - -
140L TYR* 1.3 64.4 + - - +
141L SER 4.7 0.9 + - - -
144L ASP* 6.1 0.5 - - - +
145L GLY 3.9 0.9 + - - +
146L ALA* 3.6 1.9 - - - -
147L GLN* 3.0 40.1 + - - +
216L VAL* 3.8 9.3 - - - +
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Residues in contact with TYR 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L LYS 4.7 3.4 - - - -
43L ASP* 3.6 23.1 - - - +
44L GLY* 4.5 1.8 - - - -
72L HIS* 4.4 8.8 - - - +
139L SER* 1.3 79.3 - - - +
141L SER* 1.3 82.6 + - - +
142L VAL* 3.9 24.6 - - + +
145L GLY* 3.5 14.5 - - - -
146L ALA* 3.5 23.3 - - + -
216L VAL* 3.7 8.2 - - + +
217L GLY* 3.4 22.4 - - - +
218L GLU* 3.2 44.8 + - + +
221L ASN 5.8 0.4 - - - -
222L GLY* 3.4 27.8 - - - +
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Residues in contact with SER 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L HIS* 5.7 4.7 - - - -
105L ASN* 5.7 7.6 - - - -
139L SER* 4.4 1.8 + - - -
140L TYR* 1.3 87.4 - - - +
142L VAL* 1.3 61.4 + - - +
143L ASN* 3.7 5.8 + - - +
144L ASP* 3.5 28.7 + - - +
145L GLY* 2.9 31.1 + - - +
222L GLY* 5.2 2.5 - - - -
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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