Contacts of the strand formed by residues 107 - 121 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A GLU* 3.5 3.9 - - - -
78A LYS* 2.7 40.4 + - - +
81A TRP* 3.6 27.1 - - + +
89A MSE 4.3 10.8 - - + -
103A LEU* 5.7 3.8 - - + -
104A LEU 5.5 1.8 - - - +
106A SER* 1.3 78.5 - - - +
108A HIS* 1.3 64.2 + - - +
109A VAL* 3.6 1.7 + - + -
200A VAL* 3.3 33.7 - - + -
201A ILE 3.7 13.0 - - - +
202A CYS* 4.0 23.3 - - + -
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Residues in contact with HIS 108 (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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70A ILE* 5.0 2.0 - - + -
75A GLU* 3.0 33.1 + - + +
76A THR 3.8 4.7 - - - -
77A GLU* 3.5 28.0 + - - +
106A SER 4.3 0.6 + - - -
107A VAL* 1.3 70.1 - - - +
109A VAL* 1.3 71.4 + - - +
110A LEU* 4.0 19.0 - - + +
199A SER 3.7 0.9 - - - +
200A VAL* 3.4 2.6 - - - -
201A ILE* 2.6 50.7 + - + +
203A ARG* 3.4 31.2 + - - +
302A AKG 3.5 23.9 + - - -
66B TRP* 4.2 10.4 - + + -
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Residues in contact with VAL 109 (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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52A LEU* 3.8 39.7 - - + -
56A LEU* 4.0 29.1 - - + +
75A GLU* 3.2 9.5 - - - +
76A THR* 2.9 49.6 + - + +
78A LYS* 4.4 7.6 - - + -
81A TRP* 4.5 8.1 - - + -
107A VAL 4.2 8.1 - - - +
108A HIS* 1.3 78.7 - - - +
110A LEU* 1.3 60.0 + - - +
198A ILE* 4.1 5.2 - - + -
199A SER 3.4 8.7 - - - +
200A VAL* 4.5 6.1 - - + -
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Residues in contact with LEU 110 (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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70A ILE* 4.1 10.3 - - + -
73A PHE* 4.0 35.2 - - + -
74A ARG 3.9 2.5 - - - +
75A GLU* 4.2 2.0 - - + +
108A HIS* 4.0 23.7 - - + +
109A VAL* 1.3 78.0 - - - +
111A ASP* 1.3 60.3 + - - +
112A LEU* 4.0 16.6 - - + -
118A ILE* 3.7 30.3 - - + -
197A ARG 3.7 0.9 - - - +
198A ILE* 3.3 4.0 - - - +
199A SER* 2.7 57.2 + - - +
201A ILE* 4.1 2.2 - - + -
302A AKG 4.0 16.4 - - + +
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Residues in contact with ASP 111 (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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56A LEU* 3.9 18.9 - - + +
61A TYR* 2.7 21.4 + - - -
73A PHE* 3.4 2.3 - - - -
74A ARG* 2.6 70.2 + - + +
109A VAL 4.2 0.4 - - - -
110A LEU* 1.3 72.5 - - - +
112A LEU* 1.3 64.0 + - - +
196A ARG* 2.7 40.1 + - - +
197A ARG 3.6 3.8 - - - +
198A ILE* 4.3 3.1 - - + +
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Residues in contact with LEU 112 (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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70A ILE* 3.7 29.4 - - + -
71A HIS 4.0 11.7 - - - +
72A GLY 3.5 2.2 - - - +
73A PHE* 3.8 12.3 - - + -
110A LEU* 4.2 13.9 - - + +
111A ASP* 1.3 75.3 + - - +
113A GLU* 1.3 67.0 + - - +
116A GLY 4.6 0.9 - - - -
117A TYR 4.3 8.7 - - - +
118A ILE* 4.3 14.4 - - + -
179A ILE* 4.3 12.6 - - + -
194A ARG* 4.0 15.9 - - - +
196A ARG* 3.2 4.5 - - - +
197A ARG* 2.8 66.9 + - + +
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Residues in contact with GLU 113 (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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61A TYR* 3.9 41.7 - - + +
64A ASP* 5.5 1.0 - - - +
72A GLY* 3.0 39.5 + - - +
112A LEU* 1.3 73.4 - - - +
114A ALA* 1.3 58.4 + - - +
115A ARG* 3.1 9.7 - - + +
116A GLY* 2.7 30.5 + - - +
194A ARG* 3.0 13.0 + - - -
196A ARG* 4.1 4.3 - - - +
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Residues in contact with ALA 114 (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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113A GLU* 1.3 72.7 - - - +
115A ARG* 1.3 62.9 + - + +
116A GLY 3.6 1.2 + - - +
182A ASP* 4.2 8.7 + - - +
194A ARG* 3.8 28.8 + - - +
195A GLY* 3.5 32.1 - - - -
196A ARG* 3.8 8.1 - - + +
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Residues in contact with ARG 115 (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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71A HIS 5.5 0.2 - - - -
72A GLY* 5.3 1.1 - - - -
113A GLU* 3.1 12.0 - - + +
114A ALA* 1.3 80.6 - - + +
116A GLY* 1.3 61.4 + - - +
117A TYR* 3.7 15.8 - - - -
181A ARG* 5.2 3.0 - - - +
182A ASP* 5.7 4.5 - - + +
183A GLU* 5.2 18.5 + - - +
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Residues in contact with GLY 116 (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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71A HIS 3.1 15.9 - - - -
72A GLY* 3.9 13.7 - - - -
112A LEU* 4.6 3.6 - - - -
113A GLU* 2.7 16.8 + - - +
114A ALA 4.1 0.5 - - - +
115A ARG* 1.3 79.1 - - - +
117A TYR* 1.3 56.9 - - - +
181A ARG* 4.6 1.6 - - - -
194A ARG* 2.5 39.7 + - - -
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Residues in contact with TYR 117 (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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70A ILE* 4.0 0.7 - - - +
71A HIS* 3.0 65.0 + + + +
112A LEU* 4.3 6.1 - - - +
115A ARG 3.7 17.5 - - - -
116A GLY* 1.3 73.3 - - - +
118A ILE* 1.3 77.1 + - - +
119A LYS* 3.8 28.1 - - + -
179A ILE 3.3 14.6 - - - +
180A LEU* 6.2 0.2 - - - -
181A ARG* 3.4 71.0 + - + +
194A ARG* 3.9 2.9 - - - +
105C SER* 3.9 6.8 + - - -
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Residues in contact with ILE 118 (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 ALA 3.5 7.4 - - - +
70A ILE* 3.8 22.7 - - + -
110A LEU* 3.7 27.8 - - + -
112A LEU* 4.3 7.9 - - + -
117A TYR* 1.3 84.6 - - - +
119A LYS* 1.3 64.3 + - - +
121A HIS* 3.4 32.8 - - + +
177A HIS* 5.4 0.2 - - + -
178A GLU* 3.1 15.0 - - - +
179A ILE* 3.0 46.7 + - + +
180A LEU* 5.2 0.2 - - - -
302A AKG 3.7 24.2 - - + +
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Residues in contact with LYS 119 (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 TRP* 2.7 32.1 + - - +
68A ALA 3.9 6.7 - - - +
69A ALA* 2.6 17.2 + - - +
71A HIS* 3.5 17.2 + - + +
117A TYR* 3.8 28.4 + - + -
118A ILE* 1.3 74.7 - - - +
120A PRO* 1.4 77.6 - - + +
121A HIS* 3.1 19.4 + - - +
177A HIS 3.3 2.9 - - - +
178A GLU* 3.8 1.6 - - - -
181A ARG* 4.9 7.2 - - - +
104C LEU* 4.9 15.3 - - - +
127C PHE* 3.5 33.3 - - + +
205C LEU* 6.2 2.9 - - - -
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Residues in contact with PRO 120 (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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119A LYS* 1.4 90.4 - - + +
121A HIS* 1.3 62.0 + - - +
146A VAL* 6.1 1.1 - - + -
176A SER* 3.8 19.1 - - - +
177A HIS 3.3 8.5 - - - +
178A GLU* 3.4 30.7 - - + +
126C LYS* 5.4 6.4 - - - +
127C PHE* 3.8 17.0 - - + -
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Residues in contact with HIS 121 (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 ALA* 3.9 19.2 - - + +
70A ILE* 5.4 0.9 - - + -
118A ILE* 3.4 20.9 - - + +
119A LYS 3.1 17.9 + - - +
120A PRO* 1.3 75.8 - - - +
122A VAL* 1.3 70.3 + - - +
123A ASP* 2.7 15.9 + - - -
176A SER* 3.4 6.2 - - - -
177A HIS* 2.8 41.6 + + - -
301A MN 2.1 33.0 + - - -
302A AKG 3.0 16.1 + - - -
126C LYS* 5.7 7.2 - - + -
127C PHE* 5.1 3.1 - - + -
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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