Contacts of the strand formed by residues 133 - 141 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30K VAL* 3.8 4.7 - - - -
78K ALA 3.4 14.6 - - - +
80K LEU 3.8 13.5 - - - +
83K ASP* 4.0 5.4 - - - -
84K ALA* 3.5 29.6 - - + +
87K LEU* 3.3 33.2 - - - +
119K VAL* 5.5 1.2 - - - +
131K PHE* 3.3 8.1 + - - +
132K GLY* 1.3 80.5 - - - +
134K SER* 1.3 63.5 + - - +
135K PHE* 4.5 6.3 - - - -
151K ILE 4.4 0.5 - - - +
152K ASP 4.3 1.4 - - - -
153K PRO* 3.6 19.8 - - - +
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Residues in contact with SER 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K VAL* 3.4 20.1 - - - +
77K VAL* 3.7 1.0 - - - +
78K ALA 3.0 28.9 + - - +
133K CYS* 1.3 77.1 - - - +
135K PHE* 1.3 66.2 + - - +
150K MET* 4.4 1.7 - - - -
151K ILE 3.2 11.4 - - - -
152K ASP* 3.5 10.2 - - - +
153K PRO* 3.4 17.0 - - - +
165K ILE* 3.9 25.1 - - - +
169K ARG* 4.0 7.4 + - - -
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Residues in contact with PHE 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75K MET* 3.7 26.5 - - + -
76K ALA 3.1 13.9 - - - +
77K VAL* 3.7 17.5 - - + -
87K LEU* 4.0 27.6 - - + -
115K VAL* 3.5 29.8 - - + -
119K VAL* 4.3 2.9 - - + -
133K CYS* 4.5 3.1 - - - -
134K SER* 1.3 82.2 - - - +
136K MET* 1.3 66.6 + - - +
137K LEU* 4.0 19.7 - - + -
150K MET* 3.3 4.9 - - - +
151K ILE* 2.9 78.9 + - + +
165K ILE* 4.0 2.5 - - - -
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Residues in contact with MET 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K ALA 4.5 0.2 - - - +
37K ILE* 4.2 8.5 - - - -
38K GLY* 4.0 20.0 - - - +
47K PHE* 3.8 21.8 - - + -
74K GLY 3.5 0.7 - - - +
75K MET* 3.2 6.9 - - - +
76K ALA* 2.8 41.2 + - - +
135K PHE* 1.3 80.0 - - - +
137K LEU* 1.3 60.9 - - - +
148K LEU* 4.2 10.1 - - + -
149K TYR 2.9 13.5 - - - +
150K MET* 4.0 13.7 - - + -
160K TYR* 5.7 0.2 - - + -
163K CYS* 3.4 51.4 - - + +
164K ALA 4.0 1.1 - - - +
165K ILE* 4.0 15.7 - - + -
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Residues in contact with LEU 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K PHE* 3.9 3.6 - - - -
69K VAL* 4.5 4.3 - - + -
73K VAL* 4.3 9.9 - - + -
74K GLY 3.2 4.5 - - - +
75K MET* 3.8 35.2 - - + -
91K ALA* 5.3 3.4 - - + -
108K LEU* 3.5 18.6 - - + +
111K LEU* 4.2 16.8 - - + +
112K ALA* 3.9 36.1 - - + +
115K VAL* 5.4 4.0 - - + -
135K PHE* 4.0 23.1 - - + -
136K MET* 1.3 74.9 - - - +
138K GLY* 1.3 58.1 + - - +
148K LEU* 3.4 3.1 - - - +
149K TYR* 2.7 38.0 + - + +
151K ILE* 4.4 2.9 - - + -
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Residues in contact with GLY 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K VAL* 4.6 4.7 - - - -
47K PHE* 3.5 17.8 - - - -
72K HIS 3.9 0.5 - - - +
73K VAL* 3.4 2.6 - - - -
74K GLY* 2.8 34.3 + - - -
108K LEU* 3.9 2.5 - - - -
137K LEU* 1.3 76.0 - - - +
139K SER* 1.3 60.3 + - - -
147K GLN 3.3 8.7 - - - -
148K LEU* 4.5 2.5 - - - -
216K VAL* 4.1 9.9 - - - +
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Residues in contact with SER 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K VAL* 3.9 2.6 - - - +
72K HIS* 3.1 35.5 - - - -
73K VAL* 4.2 0.2 - - - -
108K LEU* 3.7 31.5 + - - +
138K GLY* 1.3 74.7 - - - -
140K TYR* 1.3 63.8 + - - +
141K SER 4.7 0.5 + - - -
144K ASP* 6.1 0.5 - - - +
145K GLY 3.9 0.7 + - - +
146K ALA* 3.6 2.3 - - - -
147K GLN* 2.9 39.7 + - - +
216K VAL* 3.9 9.1 - - - +
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Residues in contact with TYR 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K LYS 4.7 2.9 - - - -
43K ASP* 3.6 23.3 - - - -
44K GLY* 4.4 2.2 - - - -
72K HIS* 4.0 9.0 + - - +
139K SER* 1.3 75.8 - - - +
141K SER* 1.3 82.0 + - - +
142K VAL* 3.9 24.1 + - + +
145K GLY* 3.5 14.6 - - - -
146K ALA* 3.5 24.2 - - + -
216K VAL* 3.7 9.0 - - + +
217K GLY* 3.4 22.9 - - - +
218K GLU* 3.1 45.2 + - + +
221K ASN 5.9 0.7 - - - -
222K GLY* 3.4 28.1 - - - +
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Residues in contact with SER 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K HIS* 5.7 4.9 - - - -
105K ASN* 5.7 7.2 - - - -
139K SER* 4.7 1.8 + - - -
140K TYR* 1.3 88.1 - - - +
142K VAL* 1.3 61.5 + - - +
143K ASN* 3.8 5.6 + - - +
144K ASP* 3.5 28.7 + - - +
145K GLY* 2.9 31.3 + - - +
222K GLY* 5.2 2.0 - - - -
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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