Contacts of the strand formed by residues 133 - 139 (chain A) in PDB entry 5KAL
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 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A THR* 5.3 16.2 - - + +
35A LEU* 5.9 5.2 - - + -
112A TRP* 4.4 28.7 - - + +
127A VAL* 5.1 0.7 - - + -
128A LYS* 4.4 2.7 - - - -
129A GLY* 2.9 35.7 + - - +
130A GLY 4.6 3.6 - - - +
131A GLY 3.4 4.9 + - - -
132A ALA* 1.3 82.6 - - - +
134A ASP* 1.3 76.4 + - - +
135A PHE* 4.3 16.6 - - + -
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Residues in contact with ASP 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER 4.9 1.5 - - - +
66A ASP* 3.3 19.4 - - + -
67A VAL* 3.0 23.4 + - - +
127A VAL 3.4 6.1 - - - +
128A LYS* 3.4 30.6 - - + +
129A GLY 3.7 3.1 + - - +
131A GLY 4.5 8.5 - - - +
133A VAL* 1.3 90.6 + - - +
135A PHE* 1.3 67.8 + - - +
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Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A THR* 4.4 19.3 - - + -
36A VAL* 4.0 21.3 - - + -
66A ASP* 4.3 2.4 - - - +
67A VAL* 3.0 24.5 - - + +
69A PHE* 4.0 17.3 - + + -
105A ILE* 5.2 3.1 - - + -
112A TRP* 4.0 17.9 - + - -
125A VAL 4.0 0.3 - - - +
126A ARG* 3.8 0.2 - - - -
127A VAL* 2.9 70.7 + - + +
133A VAL* 4.3 14.1 - - + -
134A ASP* 1.3 82.6 - - - +
136A ASP* 1.3 65.5 + - - +
137A ILE* 3.6 27.6 - - + -
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Residues in contact with ASP 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP* 3.9 18.5 - - - +
67A VAL 2.9 6.1 + - - +
68A ASP* 4.2 14.3 - - - +
69A PHE* 2.9 28.0 + - - +
124A VAL* 3.8 18.5 - - + +
125A VAL 3.4 4.7 - - - -
126A ARG* 3.3 43.6 + - - +
135A PHE* 1.3 80.2 + - - +
137A ILE* 1.3 67.8 + - - +
138A THR* 5.7 0.7 - - + -
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.4 14.1 - - + -
49A LEU* 5.6 1.3 - - + -
69A PHE* 3.3 17.0 - - + +
71A VAL* 4.2 10.3 - - + -
98A LEU* 4.0 7.4 - - + +
101A LEU* 4.1 22.9 - - + -
105A ILE* 4.0 22.9 - - + -
124A VAL* 3.2 6.4 - - - +
125A VAL* 2.9 41.8 + - + +
127A VAL* 4.5 4.0 - - + -
135A PHE* 3.6 31.9 - - + -
136A ASP* 1.3 81.3 - - - +
138A THR* 1.3 74.8 + - - +
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 4.3 11.3 - - + -
69A PHE 3.0 7.8 + - - +
70A VAL* 3.3 21.4 - - - +
71A VAL* 3.0 22.0 + - - +
98A LEU* 4.1 6.9 - - - +
122A VAL* 4.1 16.2 - - + -
123A PRO 3.5 22.2 - - - +
124A VAL* 3.8 13.5 - - + -
136A ASP* 5.7 1.1 - - + -
137A ILE* 1.3 83.8 - - - +
139A ALA* 1.3 64.1 + - - +
141A ARG* 5.4 4.8 - - - +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 4.0 1.6 - - - -
71A VAL* 3.6 15.3 - - + +
94A GLN* 3.3 23.3 + - + +
97A ILE* 3.9 28.3 - - + -
98A LEU* 4.1 13.9 - - + +
123A PRO 5.2 0.6 + - - -
138A THR* 1.3 80.6 + - - +
140A TYR* 1.3 79.0 + - + +
141A ARG* 3.4 7.7 + - - +
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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