Contacts of the helix formed by residues 115 - 131 (chain I) in PDB entry 2B4X
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 THR 115 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I ILE* 4.2 5.2 - - - -
23I TYR 3.4 13.0 - - - -
24I ARG* 3.8 27.8 - - - +
103I MET* 4.4 1.8 - - - -
113I GLU 3.7 7.9 - - - +
114I LYS* 1.3 76.3 - - - +
116I SER* 1.3 54.8 + - - +
117I ASP* 2.6 34.9 + - - +
118I GLN* 2.5 54.9 + - - +
119I ILE* 3.4 4.0 + - - +
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Residues in contact with SER 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I MET* 3.6 7.4 - - - -
22I ILE* 3.4 11.6 - - - +
23I TYR* 3.0 32.7 + - - -
91I LYS* 3.3 16.6 + - - -
99I LEU* 4.1 8.3 - - - +
103I MET* 3.6 29.8 - - - +
115I THR* 1.3 69.5 - - - +
117I ASP* 1.3 61.3 + - - +
118I GLN 3.6 0.2 + - - -
119I ILE* 3.6 8.3 + - - +
120I HIS* 3.0 24.4 - - - -
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Residues in contact with ASP 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ILE 4.3 15.5 - - - +
17I MET* 3.4 36.6 - - + +
22I ILE* 3.7 16.0 - - - +
115I THR* 2.6 31.8 + - - -
116I SER* 1.3 80.2 + - - +
118I GLN* 1.3 84.1 + - - +
120I HIS* 3.5 15.6 + - - +
121I PHE* 3.8 4.9 + - - +
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Residues in contact with GLN 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I PRO* 6.5 2.9 - - + -
113I GLU 4.9 0.4 - - - -
114I LYS* 3.4 34.2 + - + +
115I THR* 2.5 52.2 + - - +
117I ASP* 1.3 84.4 + - - +
119I ILE* 1.3 56.7 + - - +
120I HIS 3.0 2.5 - - - -
121I PHE* 2.6 33.9 + - + +
122I PHE* 3.0 30.0 + - + -
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Residues in contact with ILE 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I LEU* 4.5 1.9 - - + +
88I ALA* 5.6 0.4 - - + -
91I LYS* 3.8 25.4 - - - -
103I MET* 4.2 13.5 - - + -
108I PHE* 3.5 50.7 - - + +
111I ILE* 4.5 14.4 - - + -
114I LYS* 4.7 8.7 - - + -
115I THR 3.4 7.5 + - - +
116I SER 3.6 8.5 - - - +
118I GLN* 1.3 77.4 - - - +
120I HIS* 1.3 66.2 + - + +
122I PHE* 3.1 17.9 + - + +
123I PHE* 3.0 43.4 + - + -
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Residues in contact with HIS 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ILE* 5.0 7.6 - - + +
17I MET* 3.6 22.1 - - + +
88I ALA 3.3 19.7 - - - -
91I LYS* 2.4 40.9 + - - -
92I LEU* 3.7 21.1 - - + +
116I SER 3.0 22.4 - - - -
117I ASP 3.8 8.1 - - - +
118I GLN 3.0 0.6 - - - -
119I ILE* 1.3 75.0 - - + +
121I PHE* 1.3 61.1 + - - +
123I PHE* 4.0 0.9 - - - -
124I ALA* 3.1 22.9 + - - +
161I ILE* 6.0 1.6 - - + -
165I VAL* 3.7 19.3 - - + +
166I TYR* 2.6 32.0 + - + +
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Residues in contact with PHE 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I ALA* 3.0 29.2 - - + -
11I LYS* 4.3 2.0 - - - -
12I PRO* 3.6 47.1 - - + -
15I ILE* 4.8 11.1 - - + +
47I ARG* 5.1 6.7 - - + -
117I ASP 3.8 2.8 + - - +
118I GLN* 2.6 25.7 + - + +
120I HIS* 1.3 72.2 - - - +
122I PHE* 1.3 80.7 + + - -
124I ALA* 3.0 19.4 - - + +
125I LYS* 3.1 43.3 + - + +
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Residues in contact with PHE 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I ARG* 3.3 47.3 - - + +
48I VAL* 5.1 1.2 - - - +
50I GLU* 5.6 1.1 - - + -
51I LEU* 3.3 23.9 - - + +
111I ILE* 4.2 25.4 - - + -
114I LYS* 3.4 47.3 - - + -
118I GLN* 3.0 30.8 + - + -
119I ILE* 3.4 12.3 - - + +
121I PHE* 1.3 88.0 - + - +
123I PHE* 1.3 53.1 + - - +
124I ALA 3.0 1.6 - - - -
125I LYS* 2.8 11.4 + - - +
126I LEU* 2.7 34.3 + - - +
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Residues in contact with PHE 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I LEU* 3.3 15.8 - - + +
55I ASN* 3.8 22.2 - - - -
81I LEU* 4.9 1.3 - - + -
84I SER* 4.0 11.7 - - - -
85I THR* 3.5 24.5 - - - -
88I ALA* 3.7 7.4 - - + -
108I PHE* 3.4 41.1 - + - -
119I ILE* 3.0 24.0 + - + +
120I HIS 4.1 2.5 - - - +
122I PHE* 1.3 76.8 - - - +
124I ALA* 1.3 56.6 + - - +
126I LEU* 4.2 12.3 - - + -
127I ASN* 2.6 53.0 + - - +
165I VAL* 4.3 0.2 - - + -
166I TYR* 3.6 35.7 - + + +
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Residues in contact with ALA 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ILE* 3.7 25.6 - - + +
10I ALA* 4.9 9.6 - - + -
120I HIS 3.1 17.9 + - - +
121I PHE* 3.0 23.6 - - + +
123I PHE* 1.3 77.5 - - - +
125I LYS* 1.3 56.8 + - - +
128I CYS* 3.0 29.5 + - - +
164I LEU* 6.3 0.4 - - + -
165I VAL* 4.2 18.6 - - + +
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Residues in contact with LYS 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ILE 5.3 1.1 - - - +
8I CYS* 5.6 8.1 - - - +
10I ALA 4.8 4.9 - - - -
45I ASN* 3.8 30.6 + - + +
47I ARG* 5.4 4.3 - - + +
48I VAL* 4.0 16.2 - - + +
121I PHE* 3.1 45.5 + - + +
122I PHE* 2.8 12.1 + - - +
124I ALA* 1.3 77.9 - - - +
126I LEU* 1.3 61.6 + - - +
128I CYS* 3.6 8.4 + - + +
129I ARG* 3.4 27.7 + - - +
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Residues in contact with LEU 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I VAL* 3.6 32.3 - - + +
51I LEU* 4.1 18.4 - - + -
52I SER 5.3 2.9 - - - +
55I ASN* 4.1 20.9 - - - +
81I LEU* 4.6 5.8 - - + -
122I PHE 2.7 18.3 + - - +
123I PHE* 3.9 13.5 - - + +
125I LYS* 1.3 69.8 - - - +
127I ASN* 1.3 56.4 + - - +
129I ARG* 3.3 3.2 + - - +
130I LEU* 2.6 54.0 + - + +
417I LEU* 4.0 16.6 - - + -
419I THR* 3.9 23.1 - - - +
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Residues in contact with ASN 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ILE* 3.6 21.0 - - + +
81I LEU* 6.2 0.2 - - - +
85I THR* 4.2 9.5 + - - +
123I PHE* 2.6 42.0 + - - +
126I LEU* 1.3 72.3 - - - +
128I CYS* 1.3 68.1 + - - +
130I LEU* 4.0 9.0 - - - +
131I TYR* 3.1 50.9 + - + +
165I VAL 3.3 18.4 + - - +
166I TYR* 3.8 19.6 - - - +
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Residues in contact with CYS 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I ILE* 3.9 11.4 - - + +
8I CYS* 2.0 60.9 - - - -
124I ALA 3.0 18.1 + - - +
125I LYS* 3.6 10.8 - - + +
126I LEU 3.2 0.2 - - - -
127I ASN* 1.3 80.4 - - - +
129I ARG* 1.3 68.3 + - - +
130I LEU 3.4 0.2 + - - -
131I TYR 4.0 0.7 - - - -
132I ARG* 3.1 28.1 + - - +
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Residues in contact with ARG 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ALA 4.7 7.2 + - - -
44I THR* 4.6 4.4 - - - +
45I ASN* 3.4 40.1 - - - +
48I VAL* 4.6 7.4 - - - +
125I LYS* 3.4 14.2 + - - +
126I LEU 3.3 4.7 + - - +
128I CYS* 1.3 84.6 - - - +
130I LEU* 1.3 69.1 + - - +
132I ARG* 4.3 7.1 + - - +
417I LEU* 3.6 34.2 - - + +
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Residues in contact with LEU 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I LEU* 3.4 33.9 - - + -
126I LEU* 2.6 36.9 + - + +
127I ASN* 3.9 3.6 - - - +
128I CYS 3.3 0.4 - - - -
129I ARG* 1.3 78.7 - - - +
131I TYR* 1.3 82.3 + - + +
132I ARG 3.2 5.0 + - - -
140I LEU* 3.5 35.7 - - + +
414I GLU* 4.2 14.4 - - + +
417I LEU* 3.7 24.1 - - + +
419I THR* 4.8 2.9 - - + -
421I ILE* 4.7 0.9 - - + -
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Residues in contact with TYR 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I LEU* 4.2 9.8 - - + +
85I THR* 4.5 11.3 + - + +
127I ASN* 3.1 43.4 + - + +
128I CYS 4.0 3.2 - - - +
130I LEU* 1.3 82.2 - - + +
132I ARG* 1.3 58.5 + - - +
133I LYS* 3.8 3.0 - - - +
140I LEU* 3.5 48.2 - - + +
141I VAL* 4.1 3.1 - - - -
142I SER* 3.5 43.5 + - - +
219I ILE* 3.7 17.7 - - + +
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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