Contacts of the strand formed by residues 113 - 125 (chain B) in PDB entry 4KMH
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 PRO 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B THR* 3.4 20.6 + - + +
111B ASP 4.5 1.8 - - - +
112B GLY* 1.3 83.1 - - - +
114B SER* 1.3 59.9 + - - +
115B GLY 3.3 14.6 + - - +
116B PHE 4.5 2.7 - - - +
117B GLY* 3.7 21.1 - - - +
193B GLY* 4.2 1.6 - - - -
194B VAL* 3.8 7.9 - - + +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B SER* 3.4 13.0 - - - -
97B ASP* 3.2 31.5 + - - +
113B PRO* 1.3 66.1 - - - +
115B GLY* 1.3 59.4 + - - +
116B PHE 3.3 0.7 + - - -
117B GLY* 2.8 19.4 + - - -
190B THR* 3.7 5.9 + - - +
192B PHE 3.4 13.9 + - - -
193B GLY 3.5 22.0 - - - -
194B VAL 3.0 15.7 + - - +
195B VAL* 3.7 13.4 - - - +
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ASP* 3.7 14.8 - - - +
105B HIS* 3.5 30.3 - - - -
106B GLU 5.4 3.6 + - - -
108B THR* 4.9 3.0 + - - +
113B PRO* 3.3 15.8 + - - +
114B SER* 1.3 70.0 + - - +
116B PHE* 1.3 62.0 + - - -
117B GLY 3.5 0.2 + - - -
192B PHE 4.6 0.4 + - - -
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 3.2 33.4 + - + +
105B HIS* 3.9 9.6 - + - -
113B PRO* 4.5 4.2 - - - +
115B GLY* 1.3 72.7 - - - -
117B GLY* 1.3 58.6 + - - +
118B PHE* 3.3 30.6 - - + -
148B VAL* 3.5 43.5 - - + -
149B PHE* 4.0 31.9 - + - -
152B GLU* 4.1 32.1 - - + -
154B THR* 3.3 25.8 + - - -
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Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PRO* 3.7 15.3 - - - -
114B SER 2.8 17.4 + - - -
115B GLY 3.2 1.2 - - - -
116B PHE* 1.3 77.5 - - - +
118B PHE* 1.3 60.3 + - - +
194B VAL 3.6 18.5 - - - +
195B VAL* 4.2 1.3 - - - -
196B THR* 3.0 29.0 + - - +
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Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 3.2 42.2 - - + +
96B SER* 3.6 5.9 + - - -
114B SER 4.4 1.2 + - - -
116B PHE* 3.3 23.6 - - + -
117B GLY* 1.3 79.6 - - - +
119B GLU* 1.3 75.4 + - - +
120B LEU* 4.3 10.5 - - + -
148B VAL* 4.4 23.3 - - + -
154B THR* 3.6 21.5 - - - -
155B PHE* 3.7 30.5 - + + -
195B VAL* 4.0 3.5 - - - +
196B THR* 3.2 22.9 - - - +
198B LEU* 3.8 29.2 - - + -
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ILE* 3.8 13.8 - - + +
91B ILE* 5.6 0.4 - - + -
92B SER* 2.8 41.9 + - - +
93B PHE* 3.7 2.5 - - - -
94B GLY 2.8 20.2 + - - -
95B LEU* 3.0 16.5 + - - +
96B SER* 2.7 45.1 + - - +
98B LEU* 4.3 0.3 - - - +
118B PHE* 1.3 80.2 - - - +
120B LEU* 1.3 63.2 + - - +
121B THR 3.7 0.2 + - - -
195B VAL* 3.9 4.5 - - + -
196B THR 3.2 5.9 + - - -
197B PHE* 3.6 22.2 - - + -
198B LEU 3.2 18.7 + - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B LEU* 5.2 0.9 - - + -
92B SER* 2.8 35.3 + - - +
95B LEU* 3.7 22.7 - - + +
118B PHE* 4.3 14.6 - - + -
119B GLU* 1.3 73.2 - - - +
121B THR* 1.3 63.4 + - - +
141B MET* 3.2 30.6 - - + +
144B LEU* 3.9 35.2 - - + -
145B ALA 4.7 1.3 - - - +
148B VAL* 6.2 0.4 - - + -
155B PHE* 6.0 0.4 - - + -
179B LEU* 4.1 13.9 - - + -
198B LEU* 3.3 10.5 - - + +
200B ILE* 3.9 29.8 - - + -
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B HIS* 3.9 3.6 - - - -
90B TYR 3.0 13.7 - - - +
91B ILE* 4.1 15.3 - - + -
119B GLU 4.1 7.2 - - - +
120B LEU* 1.3 79.1 - - - +
122B PHE* 1.3 61.1 + - - +
141B MET* 4.1 2.0 - - - -
182B ASP* 2.7 30.8 + - - +
185B MET* 4.5 2.2 - - + -
197B PHE* 4.2 22.4 - - + -
198B LEU 2.7 7.1 + - - -
199B GLN* 3.3 17.0 - - - +
200B ILE* 2.8 33.5 + - - +
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B HIS* 3.6 1.9 - - - -
90B TYR* 2.9 50.8 + + + -
121B THR* 1.3 77.2 + - - +
123B ARG* 1.3 66.2 + - - +
124B LEU* 3.6 27.6 - - + -
136B TRP* 4.1 13.0 - + - -
137B PRO* 3.6 31.6 - - + -
140B LEU* 5.1 6.3 - - + -
141B MET* 4.6 5.6 - - + -
167B LEU* 5.1 5.8 - - + -
199B GLN* 4.5 1.8 - - - -
200B ILE* 3.2 45.8 - - + -
202B GLY 4.6 1.6 - - - -
236B THR* 3.4 43.1 - - + -
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ASN* 3.8 3.4 + - - -
87B HIS* 2.9 38.8 + - + -
88B TRP 3.4 3.4 - - - -
89B HIS* 3.3 35.1 + - + -
122B PHE* 1.3 78.6 - - - +
124B LEU* 1.3 60.3 + - - +
182B ASP* 2.8 23.8 + - - -
183B PRO* 3.8 10.4 - - - +
184B GLN* 3.2 31.9 + - - +
199B GLN* 3.1 37.4 + - - +
200B ILE 4.5 2.4 + - - +
233B TRP* 3.7 23.8 - - - -
234B LEU 4.5 0.3 - - - +
235B ILE* 3.5 13.1 - - + -
236B THR* 2.8 30.5 + - - -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B HIS* 3.1 2.4 - - - +
88B TRP* 2.7 41.5 + - + -
90B TYR* 3.9 26.2 - - + +
122B PHE* 3.6 17.5 - - + -
123B ARG* 1.3 72.7 - - - +
125B LYS* 1.3 70.8 + - - +
127B GLU* 6.0 1.3 - - - +
130B GLU* 5.1 2.9 - - - +
134B PRO* 4.2 13.0 - - + -
136B TRP* 3.4 46.4 - - + +
137B PRO* 4.2 1.6 - - + -
236B THR 3.4 15.0 - - - +
238B MET* 3.7 18.8 - - + +
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B PRO* 4.0 28.0 - - + -
86B GLU 4.0 8.5 - - - +
87B HIS* 3.8 2.0 - - - -
88B TRP* 4.8 0.2 - - - -
124B LEU* 1.3 81.4 - - - +
126B ARG* 1.3 85.8 + - - +
127B GLU* 3.5 30.0 + - - +
130B GLU* 4.2 2.1 - - - +
235B ILE* 3.5 13.2 - - + +
236B THR 2.9 18.6 + - - +
237B ASP* 3.4 33.5 + - + +
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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