Contacts of the strand formed by residues 38 - 51 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C THR 5.7 5.4 - - - +
19C THR* 5.9 1.1 - - - +
35C ALA* 3.0 34.4 + - + +
36C GLU 3.8 11.0 - - - +
37C GLY* 1.3 84.4 + - - +
39C PRO* 1.3 76.5 - - + +
40C SER* 3.5 3.6 + - - -
294C LEU* 3.2 38.0 + - + +
295C GLU* 3.3 18.5 + - - +
297C LEU* 3.1 31.3 + - + +
299C MET* 3.3 13.8 - - - +
360C PRO* 3.9 1.7 - - - +
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Residues in contact with PRO 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE 4.8 0.3 - - - +
35C ALA 5.6 0.9 + - - -
38C LYS* 1.3 91.3 - - + +
40C SER* 1.3 67.3 + - - +
41C MET* 3.8 11.4 + - - +
145C PRO* 5.9 0.7 - - + -
146C HIS 5.3 1.3 - - - +
179C TYR* 3.5 43.1 - - + -
294C LEU* 5.9 0.5 - - - +
297C LEU* 4.0 24.3 - - + +
298C LYS 3.7 24.0 - - - +
299C MET* 3.8 7.1 - - + +
360C PRO* 3.7 15.9 - - + -
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Residues in contact with SER 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE 3.3 12.3 - - - -
34C THR* 3.5 20.0 - - - +
35C ALA 4.9 0.2 + - - -
38C LYS 3.5 3.0 + - - -
39C PRO* 1.3 75.3 - - - +
41C MET* 1.3 62.6 + - - +
145C PRO* 3.8 1.6 - - - +
146C HIS* 2.9 50.8 + - - -
358C ILE 2.8 24.5 + - - -
360C PRO* 3.5 13.1 - - - +
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Residues in contact with MET 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL 3.6 1.2 - - - +
33C ILE* 2.8 50.1 + - + +
39C PRO* 3.9 12.8 - - - +
40C SER* 1.3 77.0 - - - +
42C ASP* 1.3 63.5 + - - +
43C VAL* 4.5 13.2 - - + -
143C VAL* 3.8 17.5 - - + -
144C GLU 3.6 2.7 - - - +
145C PRO* 3.6 29.4 - - - -
146C HIS* 4.0 1.5 + - - -
176C MET* 3.2 35.7 - - + -
179C TYR* 5.7 0.7 - - + -
182C VAL* 4.2 8.1 - - + -
292C VAL* 6.4 0.9 - - + -
294C LEU* 5.0 6.5 - - + -
297C LEU* 3.8 30.7 - - + -
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Residues in contact with ASP 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C SER* 2.3 29.2 + - - -
2C ARG* 3.4 3.1 + - + +
3C CYS* 2.9 35.7 + - - +
31C VAL 3.3 2.2 - - - -
32C THR* 2.8 24.8 + - - -
41C MET* 1.3 71.2 - - - +
43C VAL* 1.3 60.7 + - - +
44C TRP* 3.7 14.6 - - + -
143C VAL* 3.3 4.9 - - - +
144C GLU* 2.8 42.2 + - + +
146C HIS* 2.9 16.0 + - - -
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Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C CYS* 4.7 0.2 - - - -
23C LEU* 4.4 13.9 - - + -
25C LEU* 4.0 16.4 - - + +
30C CYS* 3.9 0.2 - - - -
31C VAL* 2.9 36.2 + - - +
33C ILE* 3.8 26.7 - - + -
41C MET* 4.5 4.7 - - + -
42C ASP* 1.3 79.8 - - - +
44C TRP* 1.3 66.8 + - - +
141C VAL* 3.8 18.6 - - + -
142C LYS 3.3 10.5 - - - +
143C VAL* 4.3 20.0 - - + -
184C LEU* 4.9 7.9 - - + -
292C VAL* 5.2 5.8 - - + -
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Residues in contact with TRP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ARG* 3.4 59.6 - - + +
25C LEU* 4.3 6.3 - - - -
29C GLY 3.5 22.0 - - - +
30C CYS* 4.0 9.0 - - - +
42C ASP* 3.7 19.5 - - + -
43C VAL* 1.3 85.2 - - - +
45C LEU* 1.3 69.7 + - - +
46C ASP* 3.2 29.2 + - - -
141C VAL* 3.4 7.0 - - - +
142C LYS* 2.9 61.6 + - + +
144C GLU* 4.0 9.0 - - + -
160C ARG* 3.5 33.4 - - + -
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 3.8 38.7 - - + +
26C GLU 4.2 11.0 + - - +
27C LEU* 3.6 32.9 - - + +
28C GLY 4.5 2.6 + - - -
29C GLY 4.9 0.7 - - - +
44C TRP* 1.3 76.7 - - - +
46C ASP* 1.3 59.6 + - - +
47C ALA 3.7 14.1 - - - +
48C ILE* 4.0 17.9 - - + -
139C TYR* 3.9 15.7 - - + -
140C THR 3.4 18.8 - - - +
141C VAL* 4.2 11.0 - - + -
287C HIS* 3.9 20.4 - - - -
288C VAL* 4.1 11.2 - - + -
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Residues in contact with ASP 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ARG* 5.1 3.5 + - - -
27C LEU* 3.7 7.9 - - - +
44C TRP* 3.2 26.0 + - + +
45C LEU* 1.3 74.1 - - - +
47C ALA* 1.3 61.8 + - - +
140C THR* 2.7 23.0 + - + +
142C LYS* 3.2 37.8 - - + -
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU* 3.7 8.3 - - - +
45C LEU* 3.7 2.8 - - - +
46C ASP* 1.3 84.7 - - - +
48C ILE* 1.3 70.4 + - - +
49C TYR* 4.2 9.9 - - + -
138C VAL 4.4 0.7 - - - -
139C TYR* 3.5 1.4 - - - -
140C THR* 3.0 34.2 + - - -
282C HIS* 3.9 26.0 - - + +
283C LEU 5.7 0.2 - - - -
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Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LEU* 4.0 14.9 - - + +
45C LEU* 4.0 13.7 - - + -
47C ALA* 1.3 80.8 - - - +
49C TYR* 1.3 65.6 + - - +
137C ILE* 3.8 24.7 - - + -
138C VAL 3.3 4.7 - - - +
139C TYR* 3.5 45.3 - - + +
192C VAL* 4.7 2.7 - - + -
282C HIS* 3.2 3.9 + - - +
283C LEU* 2.9 45.9 + - + -
285C SER 4.6 2.5 - - - +
286C GLY* 3.9 28.7 - - - -
287C HIS 4.1 0.2 - - - +
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Residues in contact with TYR 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ALA* 4.2 8.7 - - + -
48C ILE* 1.3 80.4 - - - +
50C GLN* 1.3 65.9 + - - +
51C GLU* 4.2 11.1 + - + -
132C TYR* 4.4 2.2 - - - -
137C ILE* 3.5 6.1 - - - +
138C VAL* 2.7 68.0 + - + +
140C THR* 3.9 20.4 + - - -
164C SER* 4.9 2.4 + - - -
280C LYS* 3.7 45.3 + - + -
281C TYR 3.2 21.3 - - - +
282C HIS* 3.8 25.1 - + + +
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Residues in contact with GLN 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C TYR* 1.3 82.1 - - - +
51C GLU* 1.3 70.8 + - - +
52C ASN 4.4 1.2 + - - -
53C PRO* 3.6 32.0 - - + +
54C ALA 4.7 1.4 - - - +
131C VAL 4.7 1.2 + - - -
132C TYR* 3.3 24.6 - - + -
133C ASP* 2.8 38.9 + - - +
136C LYS* 3.8 42.6 - - + +
137C ILE* 4.2 3.5 + - - -
138C VAL* 5.5 0.7 - - - -
281C TYR* 2.9 26.3 + - - +
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C TYR* 4.2 11.5 + - + -
50C GLN* 1.3 84.7 + - - +
52C ASN* 1.3 82.1 + - - +
53C PRO 3.3 0.5 - - - -
136C LYS 5.2 0.6 + - - -
138C VAL* 6.1 0.4 - - - +
279C THR* 3.2 23.0 + - - +
280C LYS* 3.6 35.8 - - + -
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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