Contacts of the strand formed by residues 16 - 25 (chain A) in PDB entry 4ES7
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 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TYR* 1.3 80.3 - - - +
17A LYS* 1.3 61.2 - - - -
18A TRP* 3.6 8.1 - - - -
43A VAL* 3.5 8.4 - - - -
44A LEU 3.0 33.3 + - - -
127A ARG* 3.6 3.1 - - - -
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Residues in contact with LYS 17 (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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16A GLY* 1.3 71.7 - - - -
18A TRP* 1.3 69.1 + - - +
19A TYR* 3.8 20.6 - - + +
41A THR* 4.4 10.8 + - - -
42A LEU 3.4 9.9 - - - +
43A VAL* 3.9 23.5 - - + +
127A ARG* 3.0 33.2 + - - +
161A GLU* 3.3 36.3 + - - -
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Residues in contact with TRP 18 (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 ILE* 2.8 42.4 + - + +
16A GLY 3.6 14.4 - - - -
17A LYS* 1.3 73.0 - - - +
19A TYR* 1.3 65.0 + - - +
41A THR* 3.4 5.9 - - - -
42A LEU* 2.8 36.1 + - + +
44A LEU* 3.9 16.9 - - + +
99A THR* 4.0 3.1 - - - -
101A TYR 3.6 11.4 - - - -
103A GLU 3.9 0.7 - - - -
104A TYR* 3.5 41.3 - - - -
105A ALA* 3.7 9.2 - - + -
107A PHE* 5.4 4.4 - + - -
125A TYR* 3.7 31.4 - + + -
126A GLY 3.4 24.0 - - - -
127A ARG* 3.2 45.4 - - + -
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Residues in contact with TYR 19 (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 LYS* 3.8 23.0 - - + +
18A TRP* 1.3 74.6 - - - +
20A ASN* 1.3 62.9 + - - +
21A LEU* 3.4 11.3 - - + +
39A VAL* 3.8 22.2 - - + -
40A SER 3.3 4.0 - - - -
41A THR* 3.7 30.3 - - + -
125A TYR* 3.1 7.3 - - - -
126A GLY 2.8 31.5 + - - +
127A ARG 3.4 22.0 - - - -
128A ALA 3.4 18.2 - - - +
129A PRO* 3.7 23.8 - - + +
158A ASP* 6.1 0.2 - - - -
161A GLU* 3.4 22.4 + - + -
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Residues in contact with ASN 20 (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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19A TYR* 1.3 70.1 - - - +
21A LEU* 1.3 59.7 - - - +
22A ALA 2.9 20.8 + - - -
23A ILE* 4.6 0.9 - - - +
37A MET* 4.4 7.1 - - - +
39A VAL* 3.3 26.2 - - - +
40A SER* 2.9 30.6 + - - +
123A LYS* 3.8 29.8 + - - +
124A LEU 2.9 19.5 + - - -
125A TYR* 3.5 22.6 - - + +
156A MET* 3.1 23.4 - - - +
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Residues in contact with LEU 21 (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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19A TYR* 3.4 12.6 - - + +
20A ASN* 1.3 77.0 - - - +
22A ALA* 1.3 64.3 + - - +
39A VAL* 3.8 24.2 - - + -
124A LEU* 2.9 16.4 + - + +
125A TYR 4.5 0.2 - - - -
126A GLY 3.9 6.1 - - - +
128A ALA 3.7 13.2 - - - +
129A PRO* 3.4 31.2 - - + +
130A GLN* 4.1 3.8 - - - -
131A LEU* 3.7 37.2 - - + +
136A LEU* 5.4 5.8 - - + +
155A THR* 3.7 8.2 - - + +
156A MET* 2.9 30.1 + - - +
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Residues in contact with ALA 22 (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 ASN* 2.9 16.6 + - - -
21A LEU* 1.3 83.6 - - - +
23A ILE* 1.3 62.8 + - - +
123A LYS* 3.5 0.5 - - - -
124A LEU* 2.9 30.6 + - + -
136A LEU* 5.6 3.6 - - + -
139A PHE* 3.7 24.7 - - + -
153A ILE* 5.6 0.9 - - + -
154A PHE 3.3 13.2 - - - +
155A THR* 4.3 9.6 - - + +
156A MET* 3.2 5.7 - - - +
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Residues in contact with ILE 23 (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 ASN* 4.9 0.2 - - - +
22A ALA* 1.3 76.4 - - - +
24A GLY* 1.3 68.3 + - - +
30A LEU* 4.4 8.7 - - + -
34A MET* 3.6 31.1 - - + +
37A MET* 3.9 26.2 - - + -
121A THR* 4.1 9.0 - - + -
122A ALA 3.2 13.5 - - - +
123A LYS* 3.7 31.2 - - + -
139A PHE* 4.0 6.5 - - - -
152A SER 4.1 0.2 - - - +
153A ILE* 3.4 2.9 - - - +
154A PHE* 2.8 42.6 + - + +
156A MET* 4.2 16.2 - - + -
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Residues in contact with GLY 24 (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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23A ILE* 1.3 75.4 - - - +
25A SER* 1.3 65.7 + - - -
34A MET* 3.9 4.5 - - - -
121A THR* 3.3 2.9 - - - +
122A ALA 2.8 31.1 + - - +
139A PHE* 4.0 3.3 - - - -
148A ILE* 3.8 14.6 - - - -
152A SER 3.0 14.1 - - - -
153A ILE* 4.0 7.2 - - - -
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Residues in contact with SER 25 (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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24A GLY* 1.3 77.9 - - - -
26A THR* 1.3 62.8 + - - +
27A CYS* 2.9 23.2 + - - +
30A LEU* 3.6 22.0 - - - +
31A LYS* 3.7 10.4 - - - +
34A MET* 3.9 7.9 - - - -
120A ILE 3.3 6.9 + - - -
121A THR* 2.7 24.6 + - - -
148A ILE* 3.6 6.7 - - - +
152A SER* 3.2 28.5 + - - -
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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