Contacts of the strand formed by residues 38 - 51 (chain B) in PDB entry 1K4R
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 THR 5.7 5.6 - - - +
19B THR* 5.9 1.3 - - - +
35B ALA* 3.0 34.1 + - + +
36B GLU 3.8 10.1 - - - +
37B GLY* 1.3 85.0 + - - +
39B PRO* 1.3 75.8 - - + +
40B SER* 3.5 4.2 + - - -
294B LEU* 3.2 38.0 + - + +
295B GLU* 3.3 17.8 + - - +
297B LEU* 3.1 30.7 + - + +
299B MET* 3.3 14.1 - - - +
360B PRO* 3.9 1.7 - - - +
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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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35B ALA 5.6 0.5 + - - -
38B LYS* 1.3 92.9 - - + +
40B SER* 1.3 68.6 + - - +
41B MET* 3.8 11.6 + - - +
145B PRO* 5.9 0.4 - - + -
146B HIS 5.3 1.1 - - - +
179B TYR* 3.5 42.8 - - + -
294B LEU* 5.9 0.5 - - - +
297B LEU* 4.0 24.7 - - + +
298B LYS 3.7 25.4 - - - +
299B MET* 3.8 6.3 - - + +
360B PRO* 3.7 15.7 - - + -
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Residues in contact with SER 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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33B ILE 3.3 12.2 + - - -
34B THR* 3.5 19.9 - - - +
35B ALA 4.9 0.3 + - - -
38B LYS 3.5 2.7 + - - -
39B PRO* 1.3 75.8 - - - +
41B MET* 1.3 62.9 + - - +
145B PRO* 3.8 1.9 - - - +
146B HIS* 2.9 50.2 + - - -
358B ILE 2.8 24.7 + - - -
360B PRO* 3.5 12.7 - - - +
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Residues in contact with MET 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL 3.6 1.2 - - - +
32B THR* 3.6 0.2 - - - -
33B ILE* 2.8 50.2 + - + +
39B PRO* 3.8 13.2 + - - +
40B SER* 1.3 77.2 - - - +
42B ASP* 1.3 62.4 + - - +
43B VAL* 4.1 13.2 - - + -
143B VAL* 3.8 16.6 - - + -
144B GLU 3.6 2.7 - - - +
145B PRO* 3.6 29.6 - - - -
146B HIS* 4.0 1.7 + - - -
176B MET* 3.2 35.9 - - + -
179B TYR* 5.8 0.4 - - - -
182B VAL* 4.2 8.3 - - + -
294B LEU* 5.0 6.1 - - + -
297B LEU* 3.8 31.0 - - + -
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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 SER* 2.3 27.9 + - - -
2B ARG* 3.4 3.1 + - + +
3B CYS* 2.9 37.3 + - - +
31B VAL 3.3 2.7 - - - -
32B THR* 2.8 24.8 + - - -
41B MET* 1.3 71.0 - - - +
43B VAL* 1.3 60.3 + - - +
44B TRP* 3.7 14.8 - - + -
143B VAL* 3.3 4.3 - - - +
144B GLU* 2.8 41.9 + - + +
146B HIS* 2.9 16.0 + - + -
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Residues in contact with VAL 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* 4.4 12.8 - - + -
25B LEU* 4.0 15.7 - - + +
30B CYS* 3.9 0.2 - - - -
31B VAL* 2.9 35.6 + - - +
33B ILE* 3.8 26.5 - - + -
41B MET* 4.5 4.5 - - + -
42B ASP* 1.3 80.5 - - - +
44B TRP* 1.3 66.5 + - - +
141B VAL* 3.8 18.2 - - + -
142B LYS 3.3 10.1 - - - +
143B VAL* 4.3 20.6 - - + -
184B LEU* 4.9 7.9 - - + -
292B VAL* 5.2 6.1 - - + -
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Residues in contact with TRP 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 59.4 - - + +
25B LEU* 4.3 7.2 - - - -
29B GLY 3.5 21.3 - - - +
30B CYS* 4.0 8.5 - - - +
42B ASP* 3.7 20.0 - - + -
43B VAL* 1.3 86.1 - - - +
45B LEU* 1.3 69.5 + - - +
46B ASP* 3.2 29.2 + - - -
141B VAL* 3.4 6.5 - - - +
142B LYS* 2.9 66.0 + - + +
144B GLU* 4.0 8.5 - - + -
160B ARG* 3.5 32.8 - - + -
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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* 3.8 37.6 - - + +
26B GLU 4.2 10.0 + - - +
27B LEU* 3.6 32.9 - - + +
28B GLY 4.5 3.1 + - - -
29B GLY 4.9 0.7 - - - +
44B TRP* 1.3 77.4 - - - +
46B ASP* 1.3 59.5 + - - +
47B ALA 3.7 13.7 - - - +
48B ILE* 4.0 17.3 - - + -
139B TYR* 3.9 16.8 - - + -
140B THR 3.4 18.4 - - - +
141B VAL* 4.2 10.3 - - + -
287B HIS* 3.9 20.9 - - - -
288B VAL* 4.1 9.6 - - + -
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Residues in contact with ASP 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* 5.1 3.6 + - - -
27B LEU* 3.7 7.6 - - - +
44B TRP* 3.2 24.7 + - + +
45B LEU* 1.3 75.2 - - - +
47B ALA* 1.3 64.8 + - - +
140B THR* 2.7 21.5 + - + +
142B LYS* 3.2 39.0 - - + +
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Residues in contact with ALA 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 LEU* 3.7 7.4 - - - +
45B LEU* 3.7 2.8 - - - +
46B ASP* 1.3 83.6 - - - +
48B ILE* 1.3 69.9 + - - +
49B TYR* 4.2 10.1 - - + -
138B VAL 4.4 0.9 - - - -
139B TYR* 3.5 1.4 - - - -
140B THR* 3.0 35.6 + - - -
282B HIS* 3.9 25.4 - - + +
283B LEU 5.7 0.2 - - - -
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Residues in contact with ILE 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 LEU* 4.0 15.1 - - + +
45B LEU* 4.0 12.6 - - + -
47B ALA* 1.3 80.7 - - - +
49B TYR* 1.3 65.1 + - - +
137B ILE* 3.8 25.4 - - + -
138B VAL 3.3 4.5 - - - +
139B TYR* 3.5 45.3 - - + +
192B VAL* 4.7 2.7 - - + -
282B HIS* 3.2 4.1 + - - +
283B LEU* 2.9 46.0 + - + -
285B SER 4.6 2.5 - - - +
286B GLY* 3.9 28.5 - - - -
287B HIS 4.1 0.4 - - - +
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Residues in contact with TYR 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 ALA* 4.2 9.9 - - + -
48B ILE* 1.3 79.7 - - - +
50B GLN* 1.3 67.3 + - - +
51B GLU* 4.1 11.4 + - + -
132B TYR* 4.4 2.2 - - - -
137B ILE* 3.5 5.9 - - - +
138B VAL* 2.7 68.4 + - + +
140B THR* 3.9 20.5 + - - -
164B SER* 4.9 2.3 + - - -
280B LYS* 3.7 45.6 + - + -
281B TYR 3.2 21.1 - - - +
282B HIS* 3.8 25.4 - + + +
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Residues in contact with GLN 50 (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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49B TYR* 1.3 81.5 - - - +
51B GLU* 1.3 72.4 + - - +
52B ASN 4.4 1.4 + - - -
53B PRO* 3.6 32.5 - - + +
54B ALA 4.7 1.4 - - - +
131B VAL 4.7 1.0 + - - -
132B TYR* 3.3 25.4 - - + -
133B ASP* 2.8 38.9 + - - +
136B LYS* 3.8 42.8 - - + +
137B ILE* 4.2 4.2 + - - -
138B VAL* 5.5 0.4 - - - -
281B TYR* 2.9 27.1 + - - +
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Residues in contact with GLU 51 (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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49B TYR* 4.1 11.0 + - + -
50B GLN* 1.3 83.0 + - - +
52B ASN* 1.3 82.6 + - - +
53B PRO 3.3 0.5 - - - -
136B LYS* 5.2 1.0 + - - +
138B VAL* 6.1 0.4 - - - +
279B THR* 3.2 22.8 + - - +
280B LYS* 3.6 36.1 - - + -
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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