Contacts of the strand formed by residues 27 - 36 (chain B) in PDB entry 4AFZ
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 SER 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B GLU* 3.4 32.3 + - - +
20B ILE 3.2 20.6 - - - -
21B VAL* 4.1 10.3 - - - -
26B PRO* 1.3 85.8 - - - +
28B LYS* 1.3 66.5 + - - +
29B PHE* 2.9 27.2 - - - -
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU* 3.7 1.2 - - - -
20B ILE* 2.8 44.4 + - + +
22B THR* 5.7 4.0 - - + +
26B PRO 4.4 2.0 + - - +
27B SER* 1.3 78.1 - - - +
29B PHE* 1.3 72.9 + - + +
46D GLY 4.3 6.7 + - - -
47D GLU* 3.2 34.4 + - - +
48D THR* 3.3 53.0 + - + +
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TYR* 2.8 44.0 - + + +
18B LEU 3.4 5.6 - - - +
19B GLU* 3.7 22.7 - - + -
20B ILE* 4.4 1.1 - - - +
27B SER* 2.9 33.9 - - - -
28B LYS* 1.3 86.6 - - + +
30B CYS* 1.3 70.6 + - - +
180B GLY* 4.1 16.9 + - - -
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Residues in contact with CYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B TYR* 3.8 8.5 - - - -
18B LEU* 2.9 34.0 + - + +
20B ILE* 4.0 10.1 - - + -
29B PHE* 1.3 81.7 - - - +
31B GLY* 1.3 63.5 + - - +
45B HIS* 5.0 3.4 - - - -
46B CYS* 2.1 54.5 - - + -
128B TRP* 5.8 0.7 - - - -
180B GLY 3.8 10.1 - - - -
182B SER* 3.3 15.0 - - - +
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET* 4.9 5.4 - - - -
16B ALA 3.3 12.3 - - - -
17B TYR* 4.8 0.7 - - - -
18B LEU* 3.7 5.2 - - - +
30B CYS* 1.3 77.0 - - - +
32B GLY* 1.3 58.5 + - - -
42B THR* 2.9 20.3 + - - -
127B GLY* 6.1 2.5 - - - -
128B TRP* 5.0 5.8 - - - -
180B GLY 3.6 8.4 + - - -
181B ASP* 4.8 2.0 - - - -
182B SER 3.0 9.7 + - - +
183B GLY* 3.3 13.0 - - - -
184B GLY* 4.4 4.5 - - - -
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Residues in contact with GLY 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET* 3.6 7.6 - - - +
16B ALA* 2.6 35.8 + - - +
18B LEU* 4.6 0.4 - - - -
31B GLY* 1.3 74.9 - - - -
33B PHE* 1.3 60.2 + - - +
40B VAL* 4.3 4.3 - - - -
41B LEU 3.4 13.5 - - - -
42B THR* 4.1 3.6 - - - -
183B GLY 3.4 13.2 - - - -
184B GLY* 3.9 3.4 - - - +
185B PRO* 4.6 1.6 - - - -
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TYR* 3.3 18.8 - - + +
16B ALA* 4.2 0.7 - - - +
32B GLY* 1.3 75.5 - - - +
34B LEU* 1.3 63.5 + - - +
35B ILE* 3.6 30.8 + - + -
40B VAL* 3.1 9.2 - - - +
41B LEU* 2.8 65.8 + - + -
108B LEU* 4.1 17.3 - - + -
110B PHE* 5.5 1.8 - - + -
183B GLY 3.8 10.5 - - - -
185B PRO* 3.4 39.9 - - + -
192B ALA* 4.1 15.3 - - + -
195B ILE* 3.9 12.1 - - + -
212B ILE* 3.7 18.8 - - + -
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PRO 5.4 0.2 - - - +
14B TYR* 2.9 17.9 + - - +
33B PHE* 1.3 71.0 - - - +
35B ILE* 1.3 59.8 + - - +
36B ARG 3.1 22.0 - - - +
37B ARG* 4.1 11.2 - - - +
39B PHE 3.6 7.6 - - - +
40B VAL* 3.8 15.7 - - + +
55B LEU* 3.9 22.9 - - + -
95B LEU* 4.2 4.0 - - + -
99B ALA* 4.4 7.4 - - + -
101B LEU* 4.9 2.9 - - + -
105B VAL* 4.0 21.8 - - + -
106B GLY* 3.6 26.0 - - - +
107B THR* 3.3 11.8 - - + -
108B LEU* 3.0 25.6 + - - +
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Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B PHE* 3.6 35.9 + - + +
34B LEU* 1.3 78.4 - - - +
36B ARG* 1.3 79.2 + - + +
39B PHE* 2.9 21.3 + - + +
41B LEU* 4.1 13.5 - - + -
92B LEU* 3.6 28.7 - - + -
107B THR* 3.9 12.1 + - - -
108B LEU 3.8 16.4 - - - +
110B PHE* 4.3 20.0 - - + -
219B ILE* 4.1 18.4 - - + -
223B LEU* 4.1 12.6 - - + -
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Residues in contact with ARG 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.1 19.4 - - - +
35B ILE* 1.3 86.1 + - - +
37B ARG* 1.3 67.2 + - - +
38B ASN* 3.0 12.2 + - - +
39B PHE* 3.1 27.0 + - + -
107B THR* 3.8 9.9 - - - -
110B PHE* 3.5 29.1 - - - -
216B ARG* 5.7 1.8 - - - +
220B ASN* 5.6 1.4 + - - -
223B LEU* 3.5 33.2 - - + +
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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