Contacts of the helix formed by residues 107 - 126 (chain A) in PDB entry 2K7W
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 TRP 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A PHE* 3.2 5.5 - - - +
106A ASN* 1.3 80.2 + - - +
108A GLY* 1.3 57.3 + - - +
109A ARG* 3.1 4.3 - - - +
110A VAL* 2.9 47.3 + - + +
111A VAL* 3.5 6.7 + - + +
151A TRP* 3.4 31.7 - + - -
152A ILE* 4.2 10.5 - - + -
155A GLN* 2.9 37.5 + - - -
157A GLY 5.6 0.2 - - - -
158A TRP* 4.1 22.7 - + - -
160A GLY* 3.9 11.1 - - - -
161A LEU* 3.7 47.8 - - + -
164A TYR* 3.8 29.4 - + + -
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Residues in contact with GLY 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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106A ASN* 2.7 17.2 + - - -
107A TRP* 1.3 73.7 - - - +
109A ARG* 1.3 57.1 + - - +
111A VAL* 3.3 15.1 - - - +
112A ALA* 2.9 34.7 + - - +
164A TYR* 3.7 7.0 + - - -
176A PHE* 4.0 20.4 - - - -
177A VAL* 5.3 3.1 - - - +
180A VAL* 5.6 2.5 - - - -
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Residues in contact with ARG 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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95A VAL 3.3 21.6 + - - -
96A ALA* 2.7 30.3 + - - +
99A MET* 3.4 62.2 + - + +
100A PHE* 3.7 10.3 - - - +
104A ASN 4.4 10.3 - - - +
105A PHE* 6.0 0.4 - - - -
106A ASN* 3.0 18.9 + - - +
107A TRP 3.1 3.3 - - - +
108A GLY* 1.3 74.9 - - - +
110A VAL* 1.3 73.6 + - + +
112A ALA* 4.2 3.4 - - - -
113A LEU* 3.5 35.1 + - - +
143A PHE* 3.7 15.4 - - - -
148A LEU* 5.6 6.5 - - - +
151A TRP* 5.8 2.5 - - + -
180A VAL* 4.9 6.2 - - + +
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Residues in contact with VAL 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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107A TRP* 2.9 41.7 + - + +
109A ARG* 1.3 92.5 - - + +
111A VAL* 1.3 65.1 + - - +
112A ALA 3.2 1.6 - - - -
113A LEU* 3.1 11.4 + - + +
114A PHE* 3.0 40.7 + - + -
148A LEU* 4.3 21.8 - - + -
151A TRP* 4.1 16.2 - - + -
152A ILE* 6.2 0.9 - - + -
158A TRP* 5.8 3.8 - - + -
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Residues in contact with VAL 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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63A LEU* 4.3 22.7 - - + -
66A ILE* 5.2 17.7 - - + -
70A LEU* 6.1 2.2 - - + -
107A TRP* 3.5 6.5 + - + +
108A GLY* 3.3 22.4 - - - +
110A VAL* 1.3 78.4 - - - +
112A ALA* 1.3 65.3 + - - +
114A PHE* 3.2 18.0 + - + +
115A TYR* 3.2 13.3 + - - +
161A LEU* 5.9 5.6 - - + -
164A TYR* 5.2 9.0 - - + -
177A VAL* 4.4 20.4 - - + +
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Residues in contact with ALA 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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99A MET* 4.7 2.5 - - + -
108A GLY 2.9 20.0 + - - +
109A ARG 4.5 3.8 - - - +
111A VAL* 1.3 77.4 - - - +
113A LEU* 1.3 62.9 + - - +
115A TYR* 3.3 4.6 + - - +
116A PHE* 3.1 17.3 + - - +
177A VAL* 4.0 22.0 - - + +
180A VAL* 4.6 13.7 - - + -
181A LEU* 3.4 34.7 - - + +
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Residues in contact with LEU 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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92A PHE* 4.3 28.7 - - + -
95A VAL* 4.0 28.9 - - + +
96A ALA* 4.9 2.2 - - - +
99A MET* 5.1 5.1 - - + -
109A ARG* 3.5 36.7 + - - +
110A VAL* 3.1 13.4 + - + +
112A ALA* 1.3 79.9 - - - +
114A PHE* 1.3 57.9 + - + +
116A PHE* 3.2 8.7 + - + +
117A ALA* 2.8 32.1 + - + +
140A THR* 5.6 7.2 - - + +
143A PHE* 4.5 17.7 - - + -
148A LEU* 6.3 0.7 - - + -
181A LEU* 5.3 0.4 - - - -
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Residues in contact with PHE 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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26A LEU* 5.6 10.8 - - + -
27A LEU* 3.9 41.1 - - + -
30A PHE* 4.2 25.9 - + + -
63A LEU* 4.7 25.8 - - + -
110A VAL* 3.0 39.6 + - + -
111A VAL* 3.4 15.5 - - + +
112A ALA 3.2 0.4 - - - -
113A LEU* 1.3 80.5 - - + +
115A TYR* 1.3 49.8 + - - +
117A ALA* 3.4 6.3 + - + +
118A SER* 2.7 38.0 + - - -
140A THR* 5.3 9.4 - - + -
144A LEU* 5.9 6.5 - - + -
158A TRP* 6.1 8.1 - + - -
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Residues in contact with TYR 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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30A PHE* 5.6 1.6 - - - -
67A GLY* 3.3 35.4 - - - -
70A LEU* 2.8 46.0 + - + -
71A ASP* 3.8 1.1 + - + -
73A ASN* 4.9 0.9 + - - -
76A LEU* 4.4 12.5 - - + +
77A GLN* 5.5 2.6 - - - -
80A ILE* 5.0 12.2 - - + +
111A VAL 3.2 9.0 + - - +
112A ALA* 3.6 9.2 - - - +
113A LEU 3.3 0.2 - - - -
114A PHE* 1.3 78.9 - - - +
116A PHE* 1.3 64.4 + - - +
118A SER* 3.0 18.4 + - - -
119A LYS* 2.7 56.5 + - + +
181A LEU* 3.7 24.9 - - + -
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Residues in contact with PHE 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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80A ILE* 4.6 28.9 - - + -
83A VAL* 4.9 13.7 - - + -
91A VAL* 3.8 28.5 - - + -
92A PHE* 5.1 3.8 - + - -
95A VAL* 3.9 34.3 - - + -
112A ALA 3.1 13.2 + - - +
113A LEU* 3.6 15.0 - - + +
115A TYR* 1.3 79.1 - + - +
117A ALA* 1.3 64.2 + - - +
119A LYS* 3.3 6.5 + - + +
120A LEU* 3.2 55.2 + - + +
181A LEU* 4.3 15.5 - - + -
185A LEU* 5.5 7.4 - - + -
188A TRP* 6.3 0.4 - + - -
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Residues in contact with ALA 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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27A LEU* 6.1 4.0 - - + -
92A PHE* 4.3 19.5 - - + -
113A LEU* 2.8 18.1 + - + +
114A PHE* 3.8 7.6 - - + +
116A PHE* 1.3 77.9 - - - +
118A SER* 1.3 57.1 + - - +
120A LEU* 3.1 13.9 + - - +
121A VAL* 2.9 34.4 + - + +
136A ILE* 4.5 5.7 - - + +
140A THR* 4.5 16.6 - - + +
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Residues in contact with SER 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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30A PHE* 3.5 29.5 - - - -
31A ILE* 6.4 1.6 - - - -
34A ARG* 6.3 1.8 - - - -
114A PHE 2.7 23.6 + - - -
115A TYR* 3.0 21.0 + - - -
117A ALA* 1.3 75.6 - - - +
119A LYS* 1.3 55.4 + - - +
121A VAL* 3.2 8.1 + - - +
122A LEU* 2.8 43.6 + - - +
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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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71A ASP* 2.7 39.6 + - - -
77A GLN* 4.8 9.1 - - - +
80A ILE* 3.6 37.2 - - + -
115A TYR* 2.7 50.8 + - + +
116A PHE* 3.5 9.4 - - + +
117A ALA 3.2 0.2 - - - -
118A SER* 1.3 76.4 + - - +
120A LEU* 1.3 60.4 + - + +
122A LEU* 3.5 11.7 + - + +
123A LYS* 3.0 27.9 + - - +
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Residues in contact with LEU 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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80A ILE* 6.0 3.8 - - + -
83A VAL* 5.3 12.6 - - + -
85A THR* 5.7 6.3 - - + -
88A PRO* 5.6 3.4 - - + +
91A VAL* 5.2 7.9 - - + -
92A PHE* 4.7 15.9 - - + -
116A PHE* 3.3 48.2 - - + +
117A ALA* 3.1 12.0 + - - +
119A LYS* 1.3 77.6 - - + +
121A VAL* 1.3 59.6 + - - +
123A LYS* 3.2 17.2 + - + +
124A ALA* 2.9 30.8 + - - +
136A ILE* 4.1 18.4 - - + +
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Residues in contact with VAL 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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27A LEU* 6.5 0.7 - - + -
31A ILE* 4.3 33.0 - - + -
117A ALA* 2.9 22.6 + - + +
118A SER* 3.2 10.1 + - - +
120A LEU* 1.3 76.3 - - - +
122A LEU* 1.3 62.9 + - + +
124A ALA 3.3 0.3 + - - -
125A LEU* 2.8 31.1 + - + +
133A ILE* 3.3 32.1 - - + +
136A ILE* 3.9 31.6 - - + -
137A MET* 5.7 0.9 - - - +
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Residues in contact with LEU 122 (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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31A ILE* 5.8 2.5 - - + +
34A ARG* 4.0 39.0 - - + +
35A ALA 5.4 0.2 - - - +
37A ARG* 4.9 20.0 - - - +
38A MET* 4.3 16.6 - - + +
71A ASP* 6.2 0.2 - - - +
118A SER* 2.8 26.8 + - - +
119A LYS* 3.8 11.2 - - + +
121A VAL* 1.3 83.6 - - + +
123A LYS* 1.3 61.7 + - - +
125A LEU* 3.2 10.8 + - + +
126A CYS* 2.9 33.8 + - - -
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Residues in contact with LYS 123 (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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83A VAL* 5.2 7.0 - - + -
85A THR* 3.1 41.5 + - + +
119A LYS 3.0 18.7 + - - +
120A LEU* 3.4 17.3 - - + +
122A LEU* 1.3 75.2 - - - +
124A ALA* 1.3 60.7 + - - +
126A CYS* 3.1 18.8 + - - +
127A THR* 2.8 22.9 + - - +
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Residues in contact with ALA 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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120A LEU 2.9 16.1 + - - +
123A LYS* 1.3 77.7 - - - +
125A LEU* 1.3 58.1 + - - +
127A THR* 3.0 27.9 + - - -
128A LYS 3.4 2.3 + - - -
129A VAL* 3.3 16.0 + - + +
132A LEU* 3.8 31.0 - - + -
133A ILE* 3.6 19.1 - - + -
136A ILE* 4.4 4.0 - - + -
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Residues in contact with LEU 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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31A ILE* 5.9 2.5 - - + -
35A ALA* 4.0 26.2 - - + -
38A MET* 3.7 35.8 - - + +
121A VAL* 2.8 21.6 + - + +
122A LEU* 3.4 14.4 - - + +
123A LYS 3.2 0.2 - - - -
124A ALA* 1.3 76.0 - - - +
126A CYS* 1.3 58.3 + - - +
128A LYS* 3.1 22.6 + - - +
129A VAL 5.0 2.7 - - - +
130A PRO* 5.9 4.7 - - + -
133A ILE* 3.6 21.7 - - + +
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Residues in contact with CYS 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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38A MET* 3.6 26.0 - - - -
122A LEU* 2.9 27.2 + - - -
123A LYS* 3.1 12.5 + - - +
125A LEU* 1.3 76.4 - - - +
127A THR* 1.3 57.8 + - - +
128A LYS* 3.3 9.9 - - - +
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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