Contacts of the strand formed by residues 152 - 159 (chain A) in PDB entry 5GZE
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 ASN 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ILE* 5.1 0.7 - - - -
44A GLY* 3.0 3.6 - - - -
45A HIS* 2.8 67.2 + - + +
47A PRO* 3.7 19.0 - - - +
151A VAL* 1.3 78.1 + - - +
153A ILE* 1.3 63.4 + - - +
154A HIS* 4.9 6.5 - - + +
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Residues in contact with ILE 153 (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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21A ASN* 3.2 26.2 - - - +
22A PRO* 3.4 26.5 + - + +
24A ILE* 3.8 24.5 - - + +
42A ILE* 3.7 22.0 - - + -
43A ARG 3.6 8.3 - - - +
53A PHE* 5.5 1.8 - - + -
55A VAL* 6.1 0.2 - - + -
110A PHE* 4.1 7.9 - - + -
147A ILE* 4.1 15.5 - - + -
151A VAL* 3.8 23.3 + - + -
152A ASN* 1.3 78.4 - - - +
154A HIS* 1.3 62.9 + - - +
155A SER 3.7 18.2 - - - +
156A ILE* 3.8 11.9 - - + -
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Residues in contact with HIS 154 (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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20A TYR* 3.4 8.7 - - - -
21A ASN* 2.9 35.0 + - - +
43A ARG* 2.8 21.1 + - + +
44A GLY* 3.7 29.4 + - - -
45A HIS* 3.9 21.5 - - + +
109A SER* 4.2 8.5 + - - -
152A ASN* 4.7 7.8 - - + +
153A ILE* 1.3 74.6 - - - +
155A SER* 1.3 63.7 + - - +
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Residues in contact with SER 155 (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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18A ILE* 4.1 10.8 - - - -
19A ILE 3.1 12.1 - - - -
20A TYR* 4.1 15.9 - - - -
41A VAL 3.8 0.6 + - - +
42A ILE* 3.4 3.6 - - - -
43A ARG* 3.0 55.4 + - - +
153A ILE* 3.6 3.7 - - - +
154A HIS* 1.3 83.4 - - - +
156A ILE* 1.3 67.6 + - - +
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Residues in contact with ILE 156 (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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17A ASN 3.8 2.1 - - - +
18A ILE* 3.2 8.9 - - - +
19A ILE* 2.9 36.2 + - + +
22A PRO* 4.0 15.5 - - + -
26A PHE* 3.6 38.1 - - + -
40A ILE* 4.7 1.6 - - + -
41A VAL 3.3 7.0 - - - +
42A ILE* 4.3 7.9 - - + -
145A LEU* 3.5 21.5 - - + -
147A ILE* 3.7 21.5 - - + -
153A ILE* 3.8 10.8 - - + -
155A SER* 1.3 79.9 - - - +
157A GLY* 1.3 62.1 + - - +
158A PHE* 4.1 17.7 - - + -
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Residues in contact with GLY 157 (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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15A LEU* 3.9 15.5 - - - +
16A GLN 3.8 9.4 - - - -
18A ILE* 4.2 9.6 - - - -
40A ILE* 3.6 5.2 - - - +
41A VAL* 2.8 34.9 + - - +
156A ILE* 1.3 76.1 - - - +
158A PHE* 1.3 68.3 + - - -
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Residues in contact with PHE 158 (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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15A LEU* 3.2 7.8 - - - +
16A GLN* 2.8 42.6 + - + +
17A ASN 4.1 9.0 - - - -
19A ILE* 4.4 7.0 - - + -
29A THR 5.5 0.9 - - - -
30A ILE* 4.0 24.0 - - + -
31A PRO* 3.6 27.4 - - + -
34A LEU* 5.0 0.9 - - + -
39A LEU 3.4 5.2 - - - +
40A ILE* 3.9 35.7 - - + -
145A LEU* 4.2 11.0 - - + -
156A ILE* 4.1 25.8 - - + -
157A GLY* 1.3 76.7 - - - -
159A SER* 1.3 59.3 + - - +
160A PHE* 3.4 35.7 - + + -
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Residues in contact with SER 159 (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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14A ASN* 4.0 23.6 - - - -
15A LEU* 4.1 4.0 - - - +
16A GLN* 5.1 1.8 - - - -
37A GLY 4.1 1.0 - - - +
38A THR* 3.4 2.3 - - - -
39A LEU* 3.0 54.9 + - - +
158A PHE* 1.3 74.3 - - - +
160A PHE* 1.3 64.9 + - - +
161A SER 3.8 4.3 - - - +
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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