Contacts of the strand formed by residues 91 - 99 (chain C) in PDB entry 5LK5
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 LEU 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C TYR* 5.1 0.2 - - + -
84C PHE* 3.6 33.7 - - + -
86C ASN* 3.9 19.7 - - + +
89C GLN 3.7 0.6 + - - -
90C THR* 1.3 73.8 - - - +
92C VAL* 1.3 64.9 + - - +
93C VAL* 4.3 9.2 - - + -
112C LEU* 4.1 9.9 - - + -
130C ILE* 3.9 27.8 - - + -
174C LEU* 3.7 1.6 - - + +
175C ILE* 3.5 2.3 - - - -
176C VAL* 2.8 50.9 + - + +
311C PHE* 3.9 18.6 - - + -
332C ILE* 3.8 17.3 - - + -
333C THR 3.8 3.6 - - - +
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C THR* 4.0 17.3 - - + -
91C LEU* 1.3 78.9 - - - +
93C VAL* 1.3 66.9 + - - +
94C GLN* 4.7 2.5 - - + -
173C THR* 3.8 17.5 - - + -
174C LEU 3.3 9.9 - - - +
175C ILE* 4.0 15.7 - - + -
331C LEU 3.7 1.1 - - - +
332C ILE* 3.3 9.2 - - - +
333C THR* 2.8 49.8 + - + +
335C ASP 4.1 4.7 - - - +
336C GLU* 4.0 17.7 - - - +
339C ALA* 3.7 23.8 - - + -
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 4.3 13.5 - - + -
92C VAL* 1.3 75.2 - - - +
94C GLN* 1.3 63.6 + - - +
95C PHE* 4.7 4.5 - - + -
110C VAL* 4.0 27.6 - - + -
112C LEU* 3.4 35.0 - - + -
130C ILE* 5.8 1.8 - - + -
132C PHE* 3.9 11.2 - - + -
172C TYR 3.8 0.7 - - - +
173C THR* 3.4 2.4 - - - +
174C LEU* 2.8 56.3 + - + +
314C LEU* 5.0 2.7 - - + -
331C LEU 3.6 4.7 - - - +
332C ILE* 4.8 7.6 - - + +
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Residues in contact with GLN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C VAL* 4.7 4.9 - - + -
93C VAL* 1.3 78.3 - - - +
95C PHE* 1.3 70.4 + - - +
171C LEU* 3.7 20.9 - - + +
172C TYR 3.2 13.5 - - - +
173C THR* 2.8 29.5 + - + +
188C ASN* 4.5 2.3 - - - +
329C ASN 4.2 1.9 + - - +
330C PHE* 3.4 1.2 - - - +
331C LEU* 2.8 45.6 + - + +
339C ALA* 2.9 37.0 + - - +
342C PHE* 4.1 15.4 - - - -
343C GLY* 3.6 18.8 - - - +
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Residues in contact with PHE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C VAL* 4.7 1.6 - - + -
94C GLN* 1.3 83.8 - - - +
96C THR* 1.3 66.3 + - - +
97C VAL* 3.2 31.6 - - + -
108C GLY 3.4 14.1 - - - -
110C VAL* 3.8 28.3 - - + -
132C PHE* 3.6 41.5 - + - -
133C GLY* 4.2 7.6 - - - -
134C PRO* 4.5 0.9 - - + -
171C LEU* 3.7 4.1 - - - +
172C TYR* 2.9 37.4 + - + +
327C PHE* 4.5 9.6 - + - -
328C ASP 3.8 4.7 - - - +
329C ASN 3.5 9.9 - - - -
330C PHE* 3.7 26.7 - + + -
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Residues in contact with THR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C PHE* 1.3 76.0 - - - +
97C VAL* 1.3 65.9 + - - +
169C THR* 3.6 21.8 - - + +
170C HIS 3.3 5.8 - - - +
171C LEU* 3.8 23.3 - - + -
326C ILE 4.4 1.3 + - - -
327C PHE* 3.4 6.8 - - - -
328C ASP* 2.9 55.5 + - - +
329C ASN* 3.6 18.9 + - + +
347C TRP* 4.0 20.0 - - + +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C PHE* 3.2 35.7 - - + -
96C THR* 1.3 75.7 - - - +
98C LYS* 1.3 62.3 + - - +
99C HIS* 3.8 34.9 - - + +
108C GLY 3.6 9.4 - - - +
134C PRO* 4.2 7.2 - - + -
168C PHE 3.7 2.3 - - - +
169C THR* 3.6 1.3 - - - -
170C HIS* 2.8 37.6 + - - +
172C TYR* 4.1 19.0 - - + -
325C THR* 3.9 10.5 - - + -
326C ILE 3.6 3.8 - - - -
327C PHE* 4.1 8.1 - - + -
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Residues in contact with LYS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C SER 3.5 14.1 + - - -
56C PHE* 2.7 47.2 + - - -
57C TYR* 4.4 3.2 - - - +
63C ASP* 5.6 4.4 + - - +
97C VAL* 1.3 76.7 - - - +
99C HIS* 1.3 60.9 + - - +
100C GLU* 3.1 27.4 + - + +
167C GLU 3.5 14.4 - - - +
168C PHE 3.7 5.6 - - - +
169C THR* 3.3 27.1 - - + +
324C GLY 4.0 0.5 - - - +
325C THR* 3.3 1.6 - - - -
326C ILE* 2.9 50.4 + - + +
354C GLU* 3.5 13.9 + - - +
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Residues in contact with HIS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C VAL* 3.8 18.4 - - + +
98C LYS* 1.3 69.5 - - - +
100C GLU* 1.3 63.3 + - - +
101C GLN* 3.1 13.9 + - - +
102C ASN* 3.1 9.0 + - - -
103C ILE* 3.7 39.0 - - + +
106C GLY 4.9 1.1 - - - -
107C GLY 4.3 12.8 - - - -
108C GLY* 4.4 4.2 + - - -
134C PRO* 4.7 10.2 - - + +
136C ILE* 4.2 19.7 - - + +
164C LYS 4.6 8.5 - - - -
165C ASP* 5.3 1.8 - - - +
166C ASP 3.6 13.4 + - - +
167C GLU* 3.4 15.9 - - - -
168C PHE 4.3 4.4 + - - -
325C THR* 2.7 37.6 + - + +
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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