Contacts of the strand formed by residues 123 - 134 (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 LYS 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A TYR* 3.9 35.0 - - + +
117A VAL 3.2 15.3 - - - +
118A PRO* 3.8 9.2 - - + -
119A TYR* 4.4 4.8 - - - +
122A GLY* 1.3 77.0 - - - +
124A TRP* 1.3 70.7 + - - +
125A GLU* 4.6 8.0 + - - -
152A GLU* 4.0 22.4 - - - +
153A SER* 3.2 32.3 + - - +
154A ASP* 2.8 46.1 + - + +
156A PHE* 3.8 6.6 - - - +
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Residues in contact with TRP 124 (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* 4.1 22.0 - - + -
87A ALA* 3.6 16.7 - - + +
115A VAL* 3.7 20.4 - - + -
116A TYR* 3.8 0.2 - - - -
117A VAL* 2.8 71.0 + - + +
119A TYR* 4.1 15.5 + + - -
123A LYS* 1.3 79.2 - - - +
125A GLU* 1.3 68.2 + - - +
126A GLY* 4.1 4.7 - - - -
148A ALA* 3.6 33.0 - - + -
150A ILE* 3.9 25.1 - - + -
152A GLU 3.5 9.2 - - - +
153A SER* 4.0 4.9 - - - -
156A PHE* 3.3 39.0 - + + -
166A ILE* 5.0 2.6 - - + +
501A 6WD 5.7 0.6 - - - +
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Residues in contact with GLU 125 (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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115A VAL 3.3 12.8 - - - +
116A TYR* 3.3 31.7 - - + -
123A LYS* 4.6 7.1 - - - -
124A TRP* 1.3 79.6 - - - +
126A GLY* 1.3 62.4 + - - +
150A ILE* 3.5 3.6 - - - -
151A THR* 2.9 31.6 + - - +
152A GLU* 2.8 25.8 + - - +
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Residues in contact with GLY 126 (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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114A GLY* 3.3 4.2 - - - -
115A VAL* 2.8 37.2 + - - +
124A TRP* 3.9 10.1 - - - -
125A GLU* 1.3 78.6 - - - +
127A GLU* 1.3 65.5 + - - +
128A LEU 4.1 0.2 - - - -
148A ALA* 5.2 0.2 - - - -
149A ALA 3.1 15.9 - - - -
150A ILE* 4.2 0.9 - - - -
151A THR* 3.9 5.2 - - - -
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 2.6 42.9 + - - +
108A TYR* 5.7 0.2 - - - +
110A ASP* 5.7 4.4 - - - +
113A LYS 3.7 6.5 - - - +
114A GLY* 4.4 2.5 - - - -
126A GLY* 1.3 77.4 - - - +
128A LEU* 1.3 65.5 + - - +
147A ILE 3.7 0.5 - - - +
148A ALA* 3.7 0.8 - - - -
149A ALA* 2.8 32.6 + - - +
151A THR* 3.7 26.4 + - + +
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Residues in contact with LEU 128 (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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108A TYR* 4.5 4.0 + - - -
110A ASP* 3.5 9.4 - - - +
111A LEU* 3.1 34.4 + - + +
112A ARG 4.0 1.4 + - - -
113A LYS* 2.8 40.3 + - + +
115A VAL* 3.8 26.7 - - + -
127A GLU* 1.3 73.4 - - - +
129A GLY* 1.3 58.6 + - - +
147A ILE 3.7 3.6 - - - +
148A ALA* 3.9 18.8 - - + +
177A PRO* 3.9 24.9 - - + -
181A LEU* 3.8 35.9 - - + -
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Residues in contact with GLY 129 (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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108A TYR* 4.3 12.3 - - - -
109A ARG 3.1 14.4 - - - -
111A LEU* 3.8 11.3 - - - +
127A GLU 3.8 0.2 + - - -
128A LEU* 1.3 75.4 - - - +
130A THR* 1.3 60.8 + - - +
146A ASN* 3.4 6.1 - - - +
147A ILE* 2.8 39.1 + - - -
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Residues in contact with THR 130 (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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108A TYR* 3.6 5.4 - - - -
109A ARG* 2.8 44.7 + - - +
111A LEU* 4.2 14.1 - - + -
129A GLY* 1.3 74.9 - - - -
131A ASP* 1.3 64.0 + - - +
144A ARG* 3.0 32.7 + - + -
145A ALA 3.1 12.8 - - - +
146A ASN* 3.3 26.9 - - - +
147A ILE* 4.4 2.2 - - - +
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Residues in contact with ASP 131 (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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69A GLY* 3.5 14.2 - - - +
100A TYR* 2.6 27.6 + - - +
105A SER* 2.7 24.9 + - - -
107A THR* 2.7 29.5 + - - -
108A TYR* 3.4 10.7 - - - +
130A THR* 1.3 74.9 - - - +
132A LEU* 1.3 73.1 + - - +
133A VAL* 3.7 3.9 - - - +
144A ARG* 3.4 12.9 - - - +
145A ALA 2.9 30.2 + - - +
147A ILE* 3.6 12.3 - - + +
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Residues in contact with LEU 132 (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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67A THR* 3.9 0.5 + - - +
68A VAL* 3.4 4.5 - - - -
69A GLY 2.9 29.5 + - - +
70A SER* 3.6 21.8 - - - +
107A THR* 3.9 22.2 - - + +
131A ASP* 1.3 83.3 + - - +
133A VAL* 1.3 59.5 + - - +
142A THR* 3.7 20.4 - - + -
143A VAL* 3.3 6.7 - - - +
144A ARG* 3.8 34.3 - - + +
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Residues in contact with VAL 133 (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 MET* 3.6 22.0 - - + -
67A THR 3.2 10.1 - - - +
68A VAL* 4.1 3.8 - - + -
86A PHE* 3.9 24.0 - - + -
131A ASP 3.7 11.7 - - - +
132A LEU* 1.3 80.7 - - - +
134A SER* 1.3 65.9 + - - +
141A VAL 4.2 0.3 - - - +
142A THR* 3.5 3.8 - - - +
143A VAL* 2.8 38.2 + - - +
145A ALA* 3.9 11.7 - - + -
147A ILE* 3.9 11.7 - - + -
184A PHE* 3.6 27.2 - - + -
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET* 3.4 7.6 - - - +
67A THR* 2.8 45.9 + - - +
133A VAL* 1.3 73.7 + - - +
135A ILE* 1.3 67.1 + - - +
136A PRO* 4.0 2.5 - - - -
141A VAL 3.2 11.9 + - - -
142A THR* 2.9 29.1 + - - +
184A PHE* 6.2 0.4 - - - -
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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