Contacts of the strand formed by residues 91 - 99 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A PHE* 3.6 33.4 - - + -
86A ASN* 4.0 19.1 - - + +
89A GLN 3.7 0.6 + - - -
90A THR* 1.3 75.7 - - - +
92A VAL* 1.3 65.5 + - - +
93A VAL* 4.3 9.6 - - + +
112A LEU* 4.2 9.2 - - + -
130A ILE* 3.9 18.2 - - + -
174A LEU 3.7 1.0 - - - +
175A ILE* 3.5 2.1 - - - -
176A VAL* 2.8 50.1 + - + +
311A PHE* 3.9 28.9 - - + -
332A ILE* 3.8 17.3 - - + -
333A THR 3.8 3.8 - - - +
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Residues in contact with VAL 92 (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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90A THR* 4.0 13.0 - - + -
91A LEU* 1.3 77.4 - - - +
93A VAL* 1.3 66.2 + - - +
94A GLN* 4.7 2.0 - - + -
173A THR* 3.8 17.0 - - + -
174A LEU 3.3 9.6 - - - +
175A ILE* 4.2 9.6 - - + -
331A LEU 3.6 0.9 - - - +
332A ILE* 3.3 9.0 - - - +
333A THR* 2.8 49.3 + - + +
335A ASP 4.0 5.4 - - - +
336A GLU* 4.0 27.1 - - - +
339A ALA* 3.6 24.7 - - + -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.3 13.0 - - + -
92A VAL* 1.3 76.9 - - - +
94A GLN* 1.3 63.1 + - - +
95A PHE* 4.7 3.4 - - + -
110A VAL* 4.1 25.8 - - + -
112A LEU* 3.4 36.1 - - + -
130A ILE* 5.7 2.2 - - + -
132A PHE* 3.9 11.8 - - + -
172A TYR 3.8 0.5 - - - +
173A THR* 3.4 1.9 - - - +
174A LEU* 2.8 55.2 + - + +
314A LEU* 5.0 2.9 - - + -
331A LEU 3.7 4.5 - - - +
332A ILE* 4.8 8.1 - - + +
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Residues in contact with GLN 94 (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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92A VAL* 4.7 4.9 - - + -
93A VAL* 1.3 77.6 - - - +
95A PHE* 1.3 69.9 + - - +
171A LEU* 3.7 21.2 - - + +
172A TYR 3.2 12.1 - - - +
173A THR* 2.8 30.1 + - + +
188A ASN* 4.6 2.3 - - - +
329A ASN 4.2 1.9 + - - +
330A PHE* 3.4 1.4 - - - +
331A LEU* 2.8 46.6 + - + +
339A ALA* 2.9 36.6 + - - +
342A PHE* 4.1 15.4 - - - -
343A GLY* 3.6 17.4 - - - +
346A THR* 5.3 0.2 + - - -
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Residues in contact with PHE 95 (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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93A VAL* 4.7 2.0 - - + -
94A GLN* 1.3 85.7 - - - +
96A THR* 1.3 65.4 + - - +
97A VAL* 3.3 31.4 - - + -
108A GLY 3.4 14.1 - - - -
110A VAL* 3.7 39.0 - - + -
132A PHE* 3.6 36.6 - + - -
133A GLY* 4.3 7.4 - - - -
134A PRO* 4.6 0.9 - - + -
171A LEU* 3.7 3.8 - - - +
172A TYR* 2.9 36.5 + - + +
314A LEU* 6.1 0.4 - - + -
327A PHE* 4.5 7.0 - + - -
328A ASP 3.8 4.7 - - - +
329A ASN 3.5 9.9 - - - -
330A PHE* 3.7 21.1 - + + -
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Residues in contact with THR 96 (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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95A PHE* 1.3 75.8 - - - +
97A VAL* 1.3 65.2 + - - +
169A THR* 3.6 23.3 - - + +
170A HIS 3.3 6.3 - - - +
171A LEU* 3.8 23.1 - - + -
326A ILE 4.4 1.5 + - - -
327A PHE* 3.4 6.6 - - - -
328A ASP* 2.9 55.2 + - - +
329A ASN* 3.5 16.6 + - + +
347A TRP* 4.0 21.3 - - + +
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Residues in contact with VAL 97 (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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95A PHE* 3.3 34.5 - - + -
96A THR* 1.3 73.4 - - - +
98A LYS* 1.3 61.6 + - - +
99A HIS* 3.8 29.0 + - + +
108A GLY 3.6 9.2 - - - +
134A PRO* 4.2 6.7 - - + -
168A PHE 3.7 2.1 - - - +
169A THR* 3.6 1.5 - - - -
170A HIS* 2.8 39.4 + - - +
172A TYR* 4.1 18.8 - - + -
325A THR* 3.9 16.8 - - + -
326A ILE 3.6 3.4 - - - -
327A PHE* 4.0 9.4 - - + -
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Residues in contact with LYS 98 (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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53A SER* 3.5 10.5 + - - +
56A PHE* 2.7 39.1 + - - -
57A TYR* 4.4 3.0 - - - +
63A ASP* 5.6 4.2 + - - +
97A VAL* 1.3 76.5 - - - +
99A HIS* 1.3 59.3 + - - +
100A GLU* 3.1 38.4 + - + +
167A GLU 3.5 13.9 - - - +
168A PHE 3.7 6.1 - - - +
169A THR* 3.3 26.0 - - + +
324A GLY 4.0 0.7 - - - +
325A THR* 3.3 2.5 - - - -
326A ILE* 2.9 52.1 + - + +
354A GLU* 3.5 13.3 + - - +
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Residues in contact with HIS 99 (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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97A VAL* 3.8 17.5 + - + +
98A LYS* 1.3 70.7 - - - +
100A GLU* 1.3 59.8 + - - +
101A GLN* 3.0 17.1 + - - +
102A ASN* 3.2 8.8 + - - -
103A ILE* 3.7 38.3 - - + +
106A GLY 4.8 1.8 + - - -
107A GLY 4.3 12.8 - - - -
108A GLY* 4.4 3.3 + - - -
134A PRO* 4.7 11.4 + - + +
136A ILE* 4.0 20.2 - - + +
164A LYS 4.6 7.9 - - - -
165A ASP* 5.3 1.8 - - - +
166A ASP 3.6 12.7 + - - +
167A GLU* 3.4 15.5 - - - -
168A PHE 4.3 4.6 + - - -
325A THR* 2.7 38.4 + - + +
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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