Contacts of the strand formed by residues 109 - 121 (chain A) in PDB entry 1K4R
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 GLY 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A PRO* 3.7 10.0 - - - +
98A ASP* 3.7 3.5 - - - +
99A ARG* 2.8 35.2 + - - +
107A LEU 3.8 3.0 + - - -
108A PHE* 1.3 74.0 - - - +
110A LYS* 1.3 64.5 + - - -
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Residues in contact with LYS 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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75A PRO* 3.4 21.3 - - - +
96A GLN* 3.9 45.2 + - + +
97A SER 3.4 8.1 - - - +
98A ASP* 2.8 32.0 + - - +
109A GLY* 1.3 72.0 - - - -
111A GLY* 1.3 60.2 + - - +
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Residues in contact with GLY 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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73A ARG 3.3 16.2 - - - -
74A CYS 4.3 0.7 - - - -
75A PRO* 4.1 6.1 - - - -
96A GLN* 3.2 6.8 - - - -
97A SER* 2.8 37.4 + - - -
99A ARG* 4.0 10.1 - - - +
109A GLY 3.7 1.6 + - - -
110A LYS* 1.3 75.6 - - - +
112A SER* 1.3 65.8 + - - -
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Residues in contact with SER 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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72A ALA* 3.2 2.9 - - - +
73A ARG* 2.8 35.5 + - - +
74A CYS 5.0 0.8 + - - -
78A GLY 3.7 14.7 + - - -
79A PRO* 3.9 4.3 - - - -
80A ALA* 2.7 32.9 + - - +
94A ARG* 3.5 13.9 + - - -
95A ASP 3.9 7.4 + - - -
96A GLN* 4.7 3.8 - - - +
97A SER* 5.2 0.2 + - - -
111A GLY* 1.3 72.7 - - - -
113A ILE* 1.3 60.9 + - - +
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Residues in contact with ILE 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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70A VAL* 3.9 14.1 - - + -
71A ALA 3.3 11.4 - - - +
72A ALA* 4.1 4.0 - - + -
80A ALA* 4.2 1.6 - - - -
93A LYS 4.1 0.2 - - - +
94A ARG* 3.4 3.5 - - - +
95A ASP* 2.8 52.0 + - + +
96A GLN* 3.7 8.3 - - - +
97A SER* 4.0 8.1 - - - +
112A SER* 1.3 77.9 + - - +
114A VAL* 1.3 64.5 + - - +
247A PRO* 4.0 21.1 - - + -
249A ALA 3.8 21.1 - - - +
250A VAL* 3.8 6.1 - - - -
251A LYS 3.8 29.4 - - - +
252A MET* 4.3 9.4 - - + +
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Residues in contact with VAL 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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70A VAL* 3.3 4.3 - - - +
71A ALA* 2.9 52.9 + - + +
80A ALA 3.8 20.9 - - - +
81A THR 4.0 1.1 - - - +
82A LEU* 3.7 10.2 - - + +
85A GLU* 3.7 31.2 - - + +
92A CYS* 4.5 2.0 - - + -
93A LYS 3.3 13.9 - - - +
94A ARG* 3.8 19.7 - - + +
113A ILE* 1.3 76.9 - - - +
115A ALA* 1.3 66.7 + - - +
116A CYS* 4.4 4.9 - - - -
252A MET* 4.0 1.8 - - - -
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Residues in contact with ALA 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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68A THR* 5.5 0.4 - - + -
69A LYS 3.2 9.4 - - - +
70A VAL* 3.9 16.2 - - + -
92A CYS* 3.1 3.8 - - - +
93A LYS 2.9 32.5 + - - -
114A VAL* 1.3 74.3 - - - +
116A CYS* 1.3 61.4 + - - +
244A PHE* 3.9 15.5 - - + -
252A MET* 3.2 31.1 - - + +
254A VAL* 5.0 3.6 - - + -
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Residues in contact with CYS 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASP 3.8 2.0 - - - +
68A THR* 3.4 5.8 - - - +
69A LYS* 2.8 33.1 + - + +
82A LEU* 3.8 19.5 - - + -
84A GLU* 3.8 26.5 - - + -
85A GLU* 4.0 11.0 - - - -
90A THR* 4.8 0.2 - - - -
91A VAL 3.2 6.1 - - - -
92A CYS* 2.0 45.5 - - - -
114A VAL* 4.4 0.9 - - - -
115A ALA* 1.3 74.9 - - - +
117A VAL* 1.3 63.0 + - - +
244A PHE* 4.9 1.8 - - - -
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Residues in contact with VAL 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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65A LEU* 4.4 24.2 - - + -
66A SER 3.8 7.6 - - - +
67A ASP 4.4 1.8 - - - -
68A THR* 3.3 35.0 - - + +
84A GLU* 6.3 0.2 - - - -
90A THR* 3.1 6.0 - - - -
91A VAL* 2.8 46.8 + - + +
116A CYS* 1.3 76.8 - - - +
118A LYS* 1.3 68.0 + - - +
242A VAL* 4.5 2.2 - - + -
244A PHE* 4.4 4.9 - - + -
254A VAL* 3.8 29.8 - - + -
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Residues in contact with LYS 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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64A LYS 3.7 0.9 - - - +
65A LEU* 3.3 8.0 - - - +
66A SER* 2.9 46.9 + - - +
67A ASP* 3.0 38.5 + - + +
69A LYS* 6.3 1.1 - - - -
84A GLU* 5.5 7.9 - - + +
87A GLN* 5.8 2.5 - - - +
89A GLY 3.4 7.4 - - - +
90A THR* 3.9 19.7 - - + +
117A VAL* 1.3 73.5 - - - +
119A ALA* 1.3 58.8 + - - +
120A ALA* 4.2 0.7 - - - -
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Residues in contact with ALA 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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63A ALA* 5.5 2.7 - - + -
64A LYS 3.8 2.7 - - - -
65A LEU* 3.9 16.2 - - + -
89A GLY* 2.9 25.2 + - - +
91A VAL* 3.9 15.5 - - + -
117A VAL 3.6 1.0 + - - +
118A LYS* 1.3 72.0 - - - +
120A ALA* 1.3 62.3 + - - +
234A ASN* 5.6 0.9 - - - +
235A TRP* 4.2 11.4 + - - +
238A ALA* 3.8 27.8 - - + -
242A VAL* 5.3 0.7 - - + -
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Residues in contact with ALA 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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60A CYS* 4.4 1.8 - - - -
63A ALA* 3.4 9.9 - - - +
64A LYS* 2.9 40.5 + - + +
118A LYS 5.7 0.4 - - - -
119A ALA* 1.3 74.3 - - - +
121A CYS* 1.3 64.7 + - - +
235A TRP* 4.1 12.8 - - - +
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Residues in contact with CYS 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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60A CYS* 2.0 52.7 - - - -
62A HIS 3.7 1.3 - - - -
64A LYS* 4.1 8.9 - - - +
120A ALA* 1.3 80.4 - - - +
122A GLU* 1.3 71.8 + - - +
123A ALA* 3.6 1.6 + - - -
125A LYS 3.6 16.6 - - - -
126A LYS* 4.5 6.5 - - + -
235A TRP* 3.5 26.6 - - + +
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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