Contacts of the strand formed by residues 169 - 176 (chain I) 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 THR 169 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63I ASP* 6.0 0.2 - - - -
96I THR* 3.6 33.7 - - + +
97I VAL 3.6 7.0 - - - +
98I LYS* 3.3 16.8 - - + +
168I PHE* 1.3 70.8 - - - +
170I HIS* 1.3 68.6 + - - +
329I ASN* 6.0 0.2 - - - +
347I TRP* 3.3 24.7 + - + -
350I THR* 4.0 18.7 - - + +
351I LYS* 5.6 1.6 - - - +
354I GLU* 2.5 38.2 + - - +
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Residues in contact with HIS 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96I THR* 3.3 4.8 - - - -
97I VAL 2.8 37.8 + - - +
164I LYS* 3.4 37.5 - - + +
166I ASP* 2.7 39.3 + - - -
168I PHE* 3.4 23.1 + - + -
169I THR* 1.3 80.4 + - - +
171I LEU* 1.3 61.4 + - - +
172I TYR* 3.8 22.2 - - + -
186I ILE* 4.7 1.3 - - + -
187I ASP* 2.8 27.9 + - - +
347I TRP* 4.3 3.1 + - - -
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Residues in contact with LEU 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I GLN* 3.7 34.3 - - + +
95I PHE 3.7 5.6 - - - +
96I THR* 3.7 21.5 - - + -
170I HIS* 1.3 70.7 - - - +
172I TYR* 1.3 60.9 + - - +
173I THR* 4.0 8.0 + - - +
185I LYS 3.7 0.3 - - - +
186I ILE* 3.2 10.6 - - - +
187I ASP* 2.8 37.4 + - - -
188I ASN* 3.7 32.3 - - + +
329I ASN 5.5 1.8 - - - +
343I GLY* 3.7 26.5 - - - -
346I THR* 4.8 2.5 - - - +
347I TRP* 3.9 23.5 - - + -
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Residues in contact with TYR 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93I VAL 3.8 0.3 - - - +
94I GLN* 3.2 5.7 - - - +
95I PHE* 2.9 44.9 + - + +
97I VAL* 4.1 15.0 - - + -
132I PHE* 3.9 16.7 - + + -
134I PRO* 3.6 35.7 - - + +
144I VAL* 3.9 24.0 - - + -
163I CYS* 3.5 5.2 - - - +
164I LYS* 3.0 35.2 + - - +
170I HIS* 3.8 25.1 - - + -
171I LEU* 1.3 73.2 - - - +
173I THR* 1.3 61.2 + - - +
184I VAL* 5.8 0.4 - - + -
185I LYS 3.6 2.5 - - - -
186I ILE* 3.8 34.5 - - + -
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Residues in contact with THR 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92I VAL* 3.8 22.9 - - + -
93I VAL 3.4 3.6 - - - +
94I GLN* 2.8 28.8 + - - +
132I PHE* 3.5 8.8 - - - -
171I LEU* 4.0 10.4 - - - +
172I TYR* 1.3 76.6 - - - +
174I LEU* 1.3 60.6 + - - +
175I ILE* 3.9 17.0 - - + -
183I GLU 3.9 0.3 - - - +
184I VAL* 3.4 5.7 - - - -
185I LYS* 2.9 56.6 + - + +
188I ASN* 4.7 3.2 + - - +
339I ALA* 4.9 2.2 - - + -
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Residues in contact with LEU 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91I LEU 3.7 1.0 - - - +
92I VAL* 3.3 6.6 - - - +
93I VAL* 2.8 46.6 + - + +
130I ILE* 4.1 26.0 - - + -
132I PHE* 3.5 33.1 - - + -
146I VAL* 3.9 25.6 - - + -
148I PHE* 5.2 1.1 - - + -
173I THR* 1.3 73.4 - - - +
175I ILE* 1.3 71.6 + - - +
176I VAL* 4.0 21.5 - - + -
182I TYR* 4.6 6.5 - - + -
183I GLU 3.7 9.0 - - - +
184I VAL* 4.0 12.1 - - + -
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Residues in contact with ILE 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I THR* 4.0 11.2 - - + -
91I LEU 3.5 2.7 - - - +
92I VAL* 4.0 11.7 - - + -
173I THR* 3.9 23.1 - - + -
174I LEU* 1.3 74.9 - - - +
176I VAL* 1.3 64.3 + - - +
177I ARG* 4.0 15.7 - - + +
182I TYR* 3.0 9.2 - - - +
183I GLU* 2.9 57.4 + - + +
185I LYS* 4.8 12.3 - - + +
336I GLU* 3.7 52.7 - - + +
339I ALA* 5.5 0.2 - - + -
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Residues in contact with VAL 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86I ASN* 4.8 3.1 + - - +
89I GLN 4.0 1.6 - - - +
90I THR* 3.4 3.2 - - - +
91I LEU* 2.8 51.9 + - + +
130I ILE* 5.0 5.8 - - + -
148I PHE* 3.8 30.5 - - + -
174I LEU* 4.0 22.7 - - + -
175I ILE* 1.3 79.2 - - - +
177I ARG* 1.3 64.6 + - - +
180I ASN* 6.0 0.2 - - - -
181I THR 3.7 5.2 - - - +
182I TYR* 4.5 2.7 - - + +
196I LEU* 5.0 3.8 - - + -
306I TYR* 3.8 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
------------------------------------------------------------
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