Contacts of the strand formed by residues 38 - 49 (chain B) in PDB entry 3UAJ
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 LYS 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B GLY* 5.4 1.1 - - - -
19B ALA* 4.6 14.1 - - - +
35B ALA* 3.0 38.4 + - + +
36B GLN 3.2 14.9 - - - +
37B GLY* 1.3 88.7 + - - +
39B PRO* 1.4 73.1 - - + +
40B THR* 4.9 0.5 + - - -
289B MET* 3.3 45.7 + - + +
290B GLU* 3.6 17.6 + - - +
292B LEU* 3.6 17.2 + - + +
294B ILE* 3.6 5.1 - - - +
354B SER* 3.4 11.6 + - - -
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Residues in contact with PRO 39 (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 THR 4.4 1.2 - - - +
35B ALA 5.3 1.5 + - - -
38B LYS* 1.4 89.0 - - + +
40B THR* 1.3 62.5 + - - +
41B LEU* 3.6 17.0 + - + +
143B VAL* 4.4 6.1 - - + -
178B TYR* 3.8 31.4 - - + -
289B MET* 3.9 12.0 - - - +
292B LEU* 4.3 14.6 - - + -
293B ARG 3.4 36.3 - - - +
294B ILE* 3.5 10.9 - - + -
354B SER* 3.9 10.1 - - - +
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Residues in contact with THR 40 (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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32B THR* 3.9 7.0 - - + -
33B THR 3.4 17.7 - - - +
34B MET* 3.9 13.5 - - + +
35B ALA 5.6 0.3 + - - -
38B LYS 4.9 0.3 + - - -
39B PRO* 1.3 71.7 - - - +
41B LEU* 1.3 59.8 + - - +
143B VAL* 3.8 6.9 - - - +
144B HIS* 3.4 46.3 + - + +
352B ILE* 2.6 43.5 + - + +
353B SER* 4.4 0.9 - - - -
354B SER* 3.3 19.6 + - - +
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Residues in contact with LEU 41 (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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31B VAL 3.9 0.2 - - - +
32B THR* 3.4 6.6 - - - +
33B THR* 3.0 39.0 + - - +
39B PRO* 3.6 11.4 + - + +
40B THR* 1.3 79.0 - - - +
42B ASP* 1.3 65.3 + - - +
43B PHE* 3.8 16.2 - - + -
141B VAL* 3.9 8.5 - - + -
142B THR 3.5 2.7 - - - -
143B VAL* 3.8 27.8 - - + -
144B HIS* 4.6 0.4 - - - -
175B LEU* 3.8 21.5 - - + -
178B TYR* 6.0 0.2 - - + -
181B LEU* 3.8 15.5 - - + -
287B VAL* 5.7 0.2 - - + -
289B MET* 4.0 14.4 - - + -
292B LEU* 3.8 29.2 - - + -
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Residues in contact with ASP 42 (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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1B MET* 2.8 31.5 + - - -
2B ARG* 3.2 15.3 + - + -
3B CYS* 3.4 26.0 - - - +
4B VAL 5.1 0.2 + - - -
9B ARG* 4.1 0.2 + - - -
30B CYS* 5.3 0.2 - - - -
31B VAL 3.5 2.5 - - - -
32B THR* 3.1 24.3 + - - +
41B LEU* 1.3 74.0 - - - +
43B PHE* 1.3 62.6 + - - +
44B GLU* 5.6 0.2 - - - -
140B VAL 3.1 7.6 - - - +
141B VAL* 3.4 1.1 - - - -
142B THR* 2.7 39.2 + - - +
144B HIS* 3.1 22.0 + - - -
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Residues in contact with PHE 43 (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 LEU* 4.0 13.2 - - + -
25B LEU* 3.7 19.4 - - + +
30B CYS* 3.7 1.8 - - - -
31B VAL 2.7 41.9 + - - +
33B THR* 3.3 42.8 - - + -
41B LEU* 3.8 11.0 - - + -
42B ASP* 1.3 74.4 - - - +
44B GLU* 1.3 61.7 + - - +
139B VAL* 4.2 15.9 - - + -
140B VAL 3.5 1.8 - - - -
141B VAL* 3.7 31.0 - - + -
181B LEU* 4.0 9.9 - - + -
183B LEU* 3.8 25.6 - - + -
287B VAL* 3.9 25.6 - - + -
289B MET* 6.1 0.2 - - + -
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Residues in contact with GLU 44 (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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2B ARG* 3.4 38.7 + - - +
6B VAL* 4.9 7.6 - - - +
25B LEU* 3.7 6.4 - - - +
28B GLY* 4.3 14.0 - - - +
29B GLY 3.6 19.0 - - - +
30B CYS* 4.1 19.9 - - - +
43B PHE* 1.3 76.1 - - - +
45B LEU* 1.3 67.4 + - - +
46B THR* 3.3 14.0 + - - +
139B VAL* 3.5 2.9 - - - +
140B VAL* 2.9 33.1 + - + +
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Residues in contact with LEU 45 (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 LEU* 4.0 23.9 - - + +
26B GLU* 4.1 25.9 + - - +
27B HIS* 3.4 48.4 - - + +
28B GLY 4.9 1.2 + - - -
44B GLU* 1.3 74.8 - - - +
46B THR* 1.3 63.4 + - - +
47B LYS 4.8 0.7 - - - +
48B THR* 3.8 10.8 - - - +
137B TYR* 3.9 24.0 - - + -
138B THR 3.6 13.9 - - - +
139B VAL* 3.8 19.1 - - + +
279B PHE 6.0 0.2 - - - +
281B GLY 5.5 3.4 - - - +
282B HIS 6.1 0.2 - - - -
283B LEU* 3.9 18.8 - - + +
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Residues in contact with THR 46 (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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2B ARG* 4.9 4.1 + - - +
27B HIS* 3.3 15.4 - - - -
44B GLU* 3.3 15.2 + - - -
45B LEU* 1.3 70.9 - - - +
47B LYS* 1.3 65.0 + - + +
138B THR* 2.9 18.0 + - + -
140B VAL* 3.3 28.8 - - + +
277B HIS 4.9 0.3 - - - +
278B MET* 5.5 3.5 - - - +
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Residues in contact with LYS 47 (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 HIS* 3.5 5.4 - - - -
45B LEU* 3.7 1.5 - - - +
46B THR* 1.3 85.3 - - + +
48B THR* 1.3 62.5 + - - +
49B THR* 3.9 18.3 - - + +
136B GLU* 3.6 3.0 - - - +
138B THR* 2.8 59.0 + - + +
163B MET* 6.1 4.0 - - - -
276B ASN* 6.3 0.2 - - - -
277B HIS* 3.4 43.2 + - + +
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Residues in contact with THR 48 (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 HIS* 3.2 26.4 + - - -
45B LEU* 3.8 3.1 - - - +
47B LYS* 1.3 73.7 + - - +
49B THR* 1.3 61.9 + - - +
135B LEU* 4.0 13.9 - - + -
136B GLU 3.5 4.9 - - - +
137B TYR* 3.3 44.5 - - + -
277B HIS* 3.5 17.1 + - - +
279B PHE* 3.3 42.2 - - + +
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Residues in contact with THR 49 (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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47B LYS* 3.9 26.7 - - - +
48B THR* 1.3 74.3 - - - +
50B ALA* 1.3 68.7 + - - +
51B LYS* 3.6 3.8 + - + +
135B LEU* 3.5 6.9 - - - -
136B GLU* 2.8 54.0 + - + +
277B HIS* 3.5 24.9 + - - -
279B PHE* 4.2 2.2 - - - -
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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