Contacts of the strand formed by residues 107 - 121 (chain B) in PDB entry 4QKB
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 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B GLU* 3.5 3.9 - - - -
78B LYS* 2.7 39.8 + - - +
81B TRP* 3.5 31.2 - - + +
89B MSE 3.8 20.4 - - + -
103B LEU* 6.1 2.0 - - + -
104B LEU 5.7 1.1 - - - +
106B SER* 1.3 74.2 - - - +
108B HIS* 1.3 65.2 + - - +
109B VAL* 3.7 1.1 + - + +
200B VAL* 3.4 33.2 - - + -
201B ILE 3.4 16.2 - - - +
202B CYS* 4.1 10.3 - - - +
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Residues in contact with HIS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 4.8 1.6 - - + -
75B GLU* 2.9 36.9 + - + +
76B THR 3.7 6.1 - - - -
77B GLU* 3.3 26.3 + - - +
106B SER 4.1 0.8 + - - -
107B VAL* 1.3 70.4 - - - +
109B VAL* 1.3 78.6 + - - +
110B LEU* 4.0 17.3 - - + +
200B VAL* 3.5 2.1 - - - -
201B ILE* 2.7 49.4 + - + +
203B ARG* 3.1 36.4 + - - +
302B AKG 3.5 19.1 - - - -
66C TRP* 4.0 8.4 - + + -
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Residues in contact with VAL 109 (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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52B LEU* 3.5 38.1 - - + -
56B LEU* 4.2 21.2 - - + +
75B GLU* 3.2 7.1 - - - +
76B THR* 2.7 57.6 + - + +
78B LYS* 4.5 8.5 - - + -
81B TRP* 4.8 1.8 - - + -
107B VAL 4.3 7.2 - - - +
108B HIS* 1.3 79.1 - - - +
110B LEU* 1.3 62.1 + - - +
198B ILE* 4.2 10.1 - - + -
199B SER 3.5 7.6 - - - +
200B VAL* 4.4 13.0 - - + -
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 3.9 17.7 - - + -
73B PHE* 3.8 38.1 - - + -
74B ARG 4.0 2.7 - - - +
75B GLU* 4.3 7.2 - - + +
108B HIS* 4.0 11.8 - - + +
109B VAL* 1.3 74.8 - - - +
111B ASP* 1.3 62.5 + - - +
112B LEU* 4.3 12.6 - - + -
118B ILE* 3.8 20.9 - - + -
197B ARG 3.6 1.6 - - - +
198B ILE* 3.2 4.3 - - - -
199B SER* 2.7 49.1 + - - +
201B ILE* 4.3 2.0 - - + -
302B AKG 3.5 31.9 - - + +
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Residues in contact with ASP 111 (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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56B LEU* 3.8 23.5 - - + +
61B TYR* 2.7 30.5 + - - -
73B PHE* 3.3 5.9 - - - -
74B ARG* 2.7 54.0 + - + +
109B VAL 4.3 0.4 + - - -
110B LEU* 1.3 72.5 - - - +
112B LEU* 1.3 69.1 + - - +
196B ARG* 3.0 31.8 + - - +
197B ARG 3.4 4.2 - - - +
198B ILE* 4.2 3.4 - - + +
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Residues in contact with LEU 112 (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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70B ILE* 3.6 31.0 - - + -
71B HIS 3.7 17.0 - - - +
72B GLY 3.5 3.8 - - - +
73B PHE* 4.1 2.9 - - + -
110B LEU* 4.0 8.7 - - + -
111B ASP* 1.3 75.5 - - - +
113B GLU* 1.3 60.6 + - - +
116B GLY 4.7 0.4 - - - -
117B TYR* 3.9 11.4 - - - +
118B ILE* 4.0 17.7 - - + -
179B ILE* 4.4 9.6 - - + -
194B ARG* 4.0 22.9 - - - +
196B ARG* 3.2 6.4 - - - +
197B ARG* 2.7 68.6 + - + +
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Residues in contact with GLU 113 (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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61B TYR* 4.2 33.2 - - + +
64B ASP* 5.7 0.2 - - - +
72B GLY* 3.1 32.9 + - - +
73B PHE 4.5 0.3 + - - -
111B ASP* 4.1 1.2 + - - -
112B LEU* 1.3 77.4 - - - +
114B ALA* 1.3 59.6 + - - +
115B ARG* 3.1 14.1 - - - +
116B GLY* 2.6 35.1 + - - +
194B ARG* 3.5 6.4 + - - -
195B GLY 4.1 1.1 - - - -
196B ARG* 4.4 7.6 - - - -
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Residues in contact with ALA 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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113B GLU* 1.3 73.2 - - - +
115B ARG* 1.3 59.7 + - - +
116B GLY 3.5 4.9 + - - +
182B ASP* 4.5 8.5 + - - +
194B ARG* 4.0 22.8 + - - +
195B GLY* 3.4 35.4 + - - -
196B ARG* 3.9 5.2 - - + +
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Residues in contact with ARG 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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72B GLY* 5.5 0.9 - - - -
113B GLU* 3.1 17.3 - - + +
114B ALA* 1.3 78.2 - - - +
116B GLY* 1.3 61.5 + - - +
117B TYR* 3.9 11.6 - - - -
181B ARG* 4.9 5.0 - - - +
182B ASP* 5.4 4.5 + - - -
183B GLU* 4.3 16.2 + - - -
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Residues in contact with GLY 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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71B HIS 3.2 16.2 - - - -
72B GLY* 3.9 12.1 - - - -
112B LEU* 4.4 3.4 - - - -
113B GLU* 2.6 24.0 + - - +
114B ALA 3.9 0.5 - - - +
115B ARG* 1.3 75.9 - - - +
117B TYR* 1.3 58.4 + - - +
181B ARG* 4.4 1.4 - - - -
194B ARG* 2.6 34.8 + - - -
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Residues in contact with TYR 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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105A SER* 3.8 10.9 + - - -
71B HIS* 2.9 67.0 + + + +
112B LEU* 3.9 8.1 - - - +
115B ARG 3.9 7.6 - - - -
116B GLY* 1.3 78.6 - - - +
118B ILE* 1.3 77.9 + - - +
119B LYS* 3.8 25.7 - - + -
179B ILE 3.5 11.9 - - - +
181B ARG* 3.3 72.8 + - + +
194B ARG* 4.1 4.0 - - - +
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Residues in contact with ILE 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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69B ALA 3.7 6.3 - - - +
70B ILE* 3.9 20.9 - - + -
110B LEU* 3.8 26.2 - - + -
112B LEU* 4.0 9.4 - - + -
117B TYR* 1.3 85.7 - - - +
119B LYS* 1.3 73.8 + - - +
121B HIS* 3.5 23.1 - - + +
177B HIS* 5.4 0.2 - - + -
178B GLU* 3.2 12.4 - - - +
179B ILE* 2.9 58.6 + - + +
302B AKG 3.8 18.4 - - + +
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Residues in contact with LYS 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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104A LEU* 4.9 9.7 - - - +
127A PHE* 3.7 38.4 + - + +
205A LEU* 5.2 13.0 - - - -
66B TRP* 2.8 28.5 + - - +
68B ALA 3.8 13.2 - - - +
69B ALA* 2.9 16.7 + - - +
71B HIS* 3.7 12.5 + - - +
117B TYR* 3.8 26.8 + - + -
118B ILE* 1.3 75.8 - - - +
120B PRO* 1.3 70.4 - - + +
121B HIS* 2.8 25.6 + - - +
177B HIS 3.4 2.8 - - - +
178B GLU* 3.7 2.0 - - - -
181B ARG* 4.8 7.6 - - - +
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Residues in contact with PRO 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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126A LYS* 5.6 3.3 - - - +
127A PHE* 3.7 16.5 - - + -
119B LYS* 1.3 91.9 - - + +
121B HIS* 1.3 62.3 + - - +
144B ARG* 6.0 0.2 - - - +
146B VAL* 6.3 0.4 - - + -
176B SER* 3.9 17.3 - - - +
177B HIS 3.5 8.3 - - - +
178B GLU* 3.7 30.9 - - + +
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Residues in contact with HIS 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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126A LYS* 6.0 7.2 - - + +
127A PHE* 4.9 5.8 - - + -
69B ALA* 4.1 19.3 - - + +
118B ILE* 3.5 19.6 - - + +
119B LYS 2.8 18.9 + - - +
120B PRO* 1.3 76.3 - - - +
122B VAL* 1.3 66.6 + - - +
123B ASP* 3.0 20.6 - - - -
176B SER* 3.3 7.3 - - - -
177B HIS* 2.8 42.2 + + - -
301B MN 2.3 31.4 + - - -
302B AKG 3.2 14.8 + - - -
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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