Contacts of the strand formed by residues 22 - 30 (chain B) in PDB entry 4PSQ
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 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B SER* 1.3 78.4 - - - +
23B THR* 1.3 62.3 + - - -
24B TRP* 3.7 6.6 + - - -
43B ALA 3.7 0.9 - - - +
44B GLU* 3.4 17.5 - - - -
45B PHE 3.1 27.9 + - - -
139B ARG* 3.4 5.4 - - - -
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Residues in contact with THR 23 (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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22B GLY* 1.3 71.4 - - - -
24B TRP* 1.3 61.2 + - - +
25B TYR* 3.6 36.2 - - + +
42B VAL* 3.8 20.9 - - + -
43B ALA 3.5 3.8 - - - +
44B GLU* 2.7 21.4 + - - +
139B ARG* 3.0 31.4 + - - +
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Residues in contact with TRP 24 (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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20B PHE* 2.8 55.0 + + - -
22B GLY 3.8 11.2 - - - -
23B THR* 1.3 72.7 - - - +
25B TYR* 1.3 62.2 + - - +
26B ALA 4.0 0.9 + - - -
42B VAL* 3.6 5.2 - - - +
43B ALA* 2.8 40.6 + - + +
45B PHE* 3.9 17.9 - + - -
109B THR* 3.9 4.5 - - - -
111B TYR 3.7 11.0 - - - -
114B TYR* 3.4 41.3 - - - -
115B ALA* 3.8 1.6 - - + -
137B PHE* 3.5 35.1 - + + -
138B SER 3.7 14.8 - - - -
139B ARG* 3.3 47.6 - - + -
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Residues in contact with TYR 25 (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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23B THR* 3.6 26.7 - - + +
24B TRP* 1.3 74.6 - - - +
26B ALA* 1.3 63.4 - - - +
27B MET* 3.4 5.1 + - + +
41B ILE 4.0 2.5 - - - -
42B VAL* 3.9 17.9 - - + +
137B PHE* 3.4 2.3 - - - -
138B SER* 2.7 49.0 + - - +
139B ARG* 3.6 19.3 - - - -
141B PRO* 3.8 41.2 - - + +
170B HIS* 3.9 26.9 - + + +
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Residues in contact with ALA 26 (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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24B TRP 4.0 0.2 + - - -
25B TYR* 1.3 69.6 - - - +
27B MET* 1.3 59.9 + - - +
28B ALA 3.7 0.2 - - - -
41B ILE* 3.1 34.7 + - + +
135B PHE* 4.0 10.1 - - + -
136B VAL 3.5 7.6 - - - +
137B PHE* 3.8 18.7 - - + -
168B ILE* 3.7 28.3 - - + +
170B HIS* 2.8 24.8 + - - -
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Residues in contact with MET 27 (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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25B TYR* 3.8 14.8 - - + +
26B ALA* 1.3 76.6 - - - +
28B ALA* 1.3 61.9 + - + +
136B VAL* 2.9 15.0 + - + +
138B SER* 3.6 23.6 - - - -
140B ASP 3.8 12.3 - - - +
141B PRO* 3.8 17.3 - - + +
142B ASN 4.5 1.6 - - - +
143B GLY* 3.8 25.1 - - - +
144B LEU* 5.0 5.4 - - + -
167B LEU* 3.4 11.3 - - + +
168B ILE* 2.9 30.6 + - - +
170B HIS* 5.1 4.9 - - + -
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Residues in contact with ALA 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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27B MET* 1.3 79.8 + - - +
29B LYS* 1.3 64.5 + - - +
135B PHE* 3.7 2.6 - - - -
136B VAL* 2.9 46.8 + - + +
156B GLN* 4.9 2.0 - - - +
165B TYR* 4.3 12.6 - - + -
166B ARG 3.3 13.7 - - - +
167B LEU* 4.2 14.4 - - + -
168B ILE* 3.7 6.7 - - - +
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Residues in contact with LYS 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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28B ALA* 1.3 78.1 - - - +
30B LYS* 1.3 60.9 - - - +
31B ASP* 2.9 35.7 + - - +
36B PHE* 4.0 8.7 - - + -
37B LEU 2.6 29.4 + - - +
38B GLN* 3.4 33.1 + - - +
41B ILE* 4.5 4.9 - - + -
134B SER 3.2 11.2 - - - +
135B PHE* 3.9 10.3 - - + -
164B GLN 4.1 0.2 - - - +
165B TYR* 3.5 6.7 - - - -
166B ARG* 2.7 49.2 + - + +
168B ILE* 3.6 23.6 - - + -
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Residues in contact with LYS 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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29B LYS* 1.3 74.1 - - - +
31B ASP* 1.3 75.3 + - - +
32B PRO* 4.5 1.4 - - - +
36B PHE* 5.0 1.0 - - - -
131B ASP* 5.2 1.0 + - - +
132B SER* 2.7 49.1 + - - +
133B TYR* 3.2 25.2 - - - +
134B SER 3.0 13.6 + - - +
161B LEU* 3.9 16.6 - - + -
164B GLN* 3.6 50.9 - - + +
165B TYR* 3.7 20.8 - - + -
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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