Contacts of the strand formed by residues 143 - 154 (chain A) in PDB entry 5KQF
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 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ASP 3.6 0.3 - - - +
132A LEU* 3.3 6.3 - - - -
133A VAL* 2.8 33.9 + - + +
141A VAL* 4.9 0.4 - - + -
142A THR* 1.3 78.8 - - - +
144A ARG* 1.3 62.8 + - - +
145A ALA* 3.6 4.5 + - + -
184A PHE* 3.8 30.5 - - + -
187A SER* 4.5 1.1 - - - +
188A LEU* 3.9 31.4 - - + +
191A GLN* 3.5 25.6 - - + +
192A THR* 3.6 27.4 - - + -
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Residues in contact with ARG 144 (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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107A THR* 3.0 46.3 + - - +
109A ARG* 3.4 47.8 - - - +
130A THR* 3.0 44.6 + - + -
131A ASP* 3.4 7.0 - - - +
132A LEU* 3.8 22.7 - - + +
143A VAL* 1.3 69.9 - - - +
145A ALA* 1.3 61.4 + - - +
187A SER* 3.9 5.2 + - - -
191A GLN* 2.9 36.7 + - - +
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Residues in contact with ALA 145 (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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86A PHE* 4.8 0.7 - - + -
130A THR* 3.1 8.3 - - - -
131A ASP 2.9 29.6 + - - +
133A VAL* 3.9 17.7 - - + -
143A VAL* 3.6 2.2 + - + +
144A ARG* 1.3 75.9 - - - +
146A ASN* 1.3 69.9 + - - +
147A ILE* 3.6 2.4 + - - +
184A PHE* 3.8 32.8 - - + -
187A SER* 4.6 10.5 - - - -
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Residues in contact with ASN 146 (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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86A PHE* 3.6 23.0 + - - +
111A LEU* 3.7 12.0 - - - +
128A LEU* 5.9 0.4 - - + -
129A GLY 3.4 3.8 - - - +
130A THR* 3.3 19.1 - - - +
145A ALA* 1.3 74.7 - - - +
147A ILE* 1.3 62.6 + - - +
148A ALA 4.3 0.2 - - - -
180A SER 5.0 0.6 + - - -
181A LEU* 3.6 29.0 - - + +
182A GLU* 3.0 51.7 + - - +
184A PHE* 5.6 1.6 + - - +
187A SER* 5.0 2.4 + - - -
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Residues in contact with ILE 147 (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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68A VAL* 4.1 14.4 - - + -
86A PHE* 3.6 18.2 - - + +
88A VAL* 3.7 34.3 - - + -
100A TYR* 4.0 20.4 - - + +
127A GLU 3.7 0.2 - - - +
128A LEU* 3.7 3.8 - - - -
129A GLY* 2.8 37.6 + - - +
130A THR 5.4 0.2 - - - -
131A ASP* 3.6 31.4 - - + +
133A VAL* 3.9 17.9 - - + -
145A ALA 3.7 7.6 - - - +
146A ASN* 1.3 80.8 - - - +
148A ALA* 1.3 66.0 + - - +
149A ALA* 3.6 2.8 + - - +
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Residues in contact with ALA 148 (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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85A ASN* 5.0 3.4 - - - +
86A PHE 2.9 16.1 + - - +
87A ALA* 3.4 1.7 - - + -
88A VAL 2.9 27.5 + - - -
115A VAL* 4.3 2.0 - - + -
124A TRP* 3.6 36.8 - - + -
126A GLY* 5.2 0.4 - - - -
127A GLU 3.7 5.4 - - - +
128A LEU* 3.9 19.7 - - + +
147A ILE* 1.3 75.1 - - - +
149A ALA* 1.3 60.9 + - - +
150A ILE 3.4 1.1 + - - -
181A LEU* 6.0 0.2 - - + -
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Residues in contact with ALA 149 (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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88A VAL* 3.7 8.1 - - - -
90A ALA* 3.6 12.6 - - + -
100A TYR* 4.6 6.7 - - + -
102A ARG* 3.6 39.9 - - - +
126A GLY* 3.1 3.0 - - - -
127A GLU 2.8 38.6 + - - +
147A ILE 3.6 2.9 + - - +
148A ALA* 1.3 69.2 - - - +
150A ILE* 1.3 62.7 + - - +
151A THR* 3.4 4.5 + - - +
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Residues in contact with ILE 150 (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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87A ALA* 3.8 20.2 - - + +
88A VAL 2.8 35.1 + - - +
89A GLY* 4.0 3.0 - - - -
90A ALA* 3.1 24.1 + - - +
91A ALA* 3.9 5.7 + - - +
124A TRP* 3.9 26.2 - - + -
125A GLU 3.5 11.0 - - - +
126A GLY* 4.2 0.4 - - - -
148A ALA 4.1 2.2 - - - +
149A ALA* 1.3 69.6 - - - +
151A THR* 1.3 62.9 + - - +
152A GLU 3.7 17.5 - - - +
153A SER* 4.3 0.4 - - - -
156A PHE* 3.5 31.4 - - + -
157A PHE* 3.9 21.3 - - + -
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Residues in contact with THR 151 (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 ALA* 5.0 2.5 - - + +
91A ALA* 4.7 16.2 - - + +
102A ARG* 4.2 11.9 - - - +
125A GLU* 2.9 21.2 + - - +
126A GLY* 3.9 6.8 - - - -
127A GLU* 3.7 31.4 + - - +
149A ALA 3.5 13.5 - - - +
150A ILE* 1.3 74.4 - - - +
152A GLU* 1.3 67.9 + - - +
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Residues in contact with GLU 152 (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 HIS* 4.7 8.8 + - - -
123A LYS* 4.0 18.6 - - - +
124A TRP* 3.5 0.3 - - - -
125A GLU* 2.8 45.2 + - + +
150A ILE* 3.7 4.3 - - - +
151A THR* 1.3 82.9 + - - +
153A SER* 1.3 89.3 + - - +
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Residues in contact with SER 153 (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 HIS* 4.1 16.0 + - - -
123A LYS* 3.2 23.9 + - - +
124A TRP* 4.0 7.9 - - - -
150A ILE* 4.3 5.3 - - - +
152A GLU* 1.3 91.6 + - - +
154A ASP* 1.3 64.0 + - - +
156A PHE* 3.9 14.8 - - - +
157A PHE* 3.5 26.5 + - - -
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Residues in contact with ASP 154 (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 HIS* 6.3 0.7 - - - -
122A GLY* 2.9 10.1 + - - -
123A LYS* 2.8 50.6 + - + +
153A SER* 1.3 77.2 - - - +
155A LYS* 1.3 90.3 + - - +
156A PHE 3.1 2.4 + - - -
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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