Contacts of the helix formed by residues 31 - 47 (chain K) in PDB entry 5D4C
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 31 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ARG* 1.3 77.6 - - - +
32K PHE* 1.3 59.7 + - - +
33K GLY 3.2 2.9 + - - -
34K VAL* 3.5 1.8 + - - -
35K THR* 2.8 18.2 + - - -
193K ASP* 3.2 12.4 + - - -
42L ARG* 2.8 32.6 + - - -
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Residues in contact with PHE 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K LEU* 4.2 20.3 - - + +
29K GLU* 3.1 34.5 + - + +
30K ARG 3.3 5.3 - - - -
31K GLY* 1.3 77.9 - - - +
33K GLY* 1.3 64.6 + - - +
34K VAL 3.2 1.3 - - - -
35K THR* 3.6 15.3 - - + -
36K LEU* 2.9 30.9 + - + +
43L ILE* 3.8 28.0 - - + -
46L SER* 4.4 9.0 - - - -
47L SER* 3.0 29.2 - - - -
217L ILE* 4.0 10.8 - - + -
218L LEU* 5.7 0.4 - - + -
221L HIS* 3.4 46.0 - + + +
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Residues in contact with GLY 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K LEU* 4.9 0.7 - - - -
32K PHE* 1.3 77.3 - - - +
34K VAL* 1.3 55.9 + - - +
37K GLY* 2.9 26.2 + - - -
179K PHE* 3.8 1.0 - - - -
181K VAL* 3.6 21.1 - - - -
193K ASP* 2.9 25.1 + - - +
195K LEU* 3.4 22.6 - - - +
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Residues in contact with VAL 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K GLY* 3.5 2.8 + - - -
33K GLY* 1.3 75.3 - - - +
35K THR* 1.3 66.3 + - - +
37K GLY 3.1 0.2 + - - -
38K ASN* 2.9 24.3 + - + -
39K PRO* 3.6 2.9 - - - +
179K PHE* 4.0 9.9 - - + -
181K VAL* 3.9 3.1 - - + +
193K ASP* 4.5 0.4 + - - -
42L ARG* 3.5 34.5 - - - +
939M ARG* 4.1 23.1 - - + +
979M THR 3.2 26.5 - - - +
980M GLY* 4.1 21.8 - - - +
981M GLU* 4.5 3.1 - - + +
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Residues in contact with THR 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K GLY 2.8 23.2 + - - -
32K PHE* 3.4 22.1 + - + -
34K VAL* 1.3 78.0 - - - +
36K LEU* 1.3 58.8 + - - +
39K PRO* 3.2 24.4 - - - +
39L PRO* 4.0 20.6 - - + +
42L ARG* 2.9 23.7 + - - +
43L ILE* 3.7 36.0 - - + +
218L LEU* 4.4 6.0 - - + +
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Residues in contact with LEU 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K LEU* 4.0 22.2 - - + -
28K LEU* 4.1 8.1 - - + -
32K PHE* 2.9 19.0 + - + +
35K THR* 1.3 75.4 - - - +
37K GLY* 1.3 67.3 + - - +
39K PRO* 3.5 7.8 - - - +
40K LEU* 3.3 23.3 - - + +
195K LEU* 3.9 10.1 - - + -
218K LEU* 5.5 2.4 - - + +
218L LEU* 4.0 24.0 - - + -
221L HIS* 3.8 47.3 - - + +
222L LEU* 4.1 21.5 - - + -
225L PHE* 4.3 9.9 - - + -
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Residues in contact with GLY 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K GLY 2.9 21.8 + - - -
34K VAL 3.1 0.2 + - - -
36K LEU* 1.3 79.5 - - - +
38K ASN* 1.3 62.5 + - - +
40K LEU* 3.5 4.5 + - - +
41K ARG* 3.2 15.4 + - - +
179K PHE* 3.6 24.2 - - - -
195K LEU* 3.8 12.5 - - - +
197K LEU* 4.3 5.9 - - - +
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Residues in contact with ASN 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K VAL 2.9 17.2 + - - +
37K GLY* 1.3 69.3 - - - +
39K PRO* 1.3 64.8 - - + +
41K ARG* 2.9 28.2 + - - +
42K ARG* 2.9 21.7 + - - +
179K PHE* 3.5 17.6 - - + -
38L ASN* 6.1 0.2 - - - +
860M HIS* 4.6 2.6 + - - -
976M ASP 4.2 1.0 - - - +
977M GLY 3.2 17.9 + - - +
978M ARG 2.8 30.1 + - - -
979M THR 3.7 4.4 - - - +
980M GLY* 3.3 32.7 + - - +
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Residues in contact with PRO 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K VAL 3.6 2.0 - - - +
35K THR* 3.2 27.4 - - - +
36K LEU 3.5 6.1 - - - +
38K ASN* 1.3 94.5 - - + +
40K LEU* 1.3 59.6 + - - +
42K ARG* 3.4 6.9 + - + +
43K ILE* 3.1 31.3 + - - +
218K LEU* 4.1 19.7 - - + -
35L THR* 4.0 24.0 - - + +
39L PRO* 3.4 24.5 - - + -
218L LEU* 6.1 0.4 - - + -
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Residues in contact with LEU 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36K LEU* 3.3 18.1 + - + +
37K GLY 3.5 7.8 + - - +
38K ASN 3.2 0.6 - - - -
39K PRO* 1.3 76.9 - - - +
41K ARG* 1.3 58.6 + - - +
43K ILE* 3.4 4.5 + - + +
44K LEU* 2.9 39.9 + - + +
195K LEU* 5.7 0.4 - - + -
197K LEU* 3.6 24.7 - - + -
211K LEU* 3.9 8.3 - - + -
214K ALA* 4.6 6.7 - - + +
215K VAL* 3.9 29.2 - - + +
218K LEU* 4.1 22.2 - - + -
222L LEU* 4.5 4.0 - - + -
225L PHE* 3.6 35.2 - - + -
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Residues in contact with ARG 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K GLY 3.2 12.9 + - - +
38K ASN* 2.9 18.4 + - - +
40K LEU* 1.3 78.9 - - - +
42K ARG* 1.3 61.8 + - - +
44K LEU* 3.4 1.3 + - - +
45K LEU* 3.0 47.7 + - + +
177K VAL* 3.2 43.3 + - + -
178K ALA* 4.9 0.9 - - - +
179K PHE* 4.3 13.5 - - + -
197K LEU* 5.1 1.0 - - + +
855M VAL 4.9 1.4 + - - -
856M GLU* 3.9 20.2 + - - +
858M MET 4.8 0.8 + - - -
860M HIS* 3.2 61.0 + - - +
864M GLY 3.5 15.8 + - - -
866M PRO* 4.8 6.5 - - - +
977M GLY* 4.2 5.5 + - - -
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Residues in contact with ARG 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K ASN* 2.9 35.6 + - - +
39K PRO* 3.7 7.9 - - - +
40K LEU 3.3 0.2 - - - -
41K ARG* 1.3 78.6 - - + +
43K ILE* 1.3 55.1 + - + +
45K LEU* 3.5 2.3 + - - +
46K SER* 2.6 33.7 + - - -
31L GLY* 3.0 25.1 + - - -
34L VAL* 3.3 17.6 - - - +
35L THR* 2.9 36.8 + - + +
856M GLU* 3.2 39.5 + - + +
857M ASP* 2.8 26.1 + - - -
977M GLY 2.9 23.5 + - - +
978M ARG* 3.3 15.0 - - - +
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Residues in contact with ILE 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K PRO 3.1 19.6 + - - +
40K LEU* 3.9 4.5 - - + +
42K ARG* 1.3 73.8 - - + +
44K LEU* 1.3 62.8 + - - +
46K SER* 3.8 4.7 - - - -
47K SER* 2.9 29.7 + - - +
48K ILE* 3.6 5.6 - - + +
214K ALA* 3.8 21.3 - - + +
217K ILE* 3.6 32.8 - - + -
218K LEU* 3.6 44.2 - - + +
32L PHE* 4.0 22.9 - - + -
35L THR* 4.1 7.2 - - + -
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Residues in contact with LEU 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K LEU* 2.9 37.2 + - + +
41K ARG 3.8 1.1 - - - +
43K ILE* 1.3 77.9 - - - +
45K LEU* 1.3 60.3 + - - +
46K SER 3.4 0.7 + - - -
48K ILE* 3.5 11.5 - - + +
172K SER* 3.9 1.9 + - - -
174K VAL* 3.2 30.3 - - + +
177K VAL* 3.7 22.9 - - + -
197K LEU* 4.8 7.0 - - + -
199K ILE* 3.6 31.0 - - + -
210K ALA* 3.7 45.3 - - + +
211K LEU* 3.8 6.1 - - + +
214K ALA* 4.0 8.3 - - + -
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Residues in contact with LEU 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K ARG* 3.0 58.4 + - + +
42K ARG 3.5 3.8 + - - +
43K ILE 3.3 0.2 - - - -
44K LEU* 1.3 76.6 - - - +
46K SER* 1.3 58.0 + - - +
172K SER* 4.1 12.1 + - - -
174K VAL* 4.4 14.2 - - + +
175K ARG 4.8 3.1 - - - +
176K ARG* 4.6 5.8 - - - -
177K VAL* 4.1 29.8 - - + +
696M LYS* 5.1 4.3 + - - -
855M VAL* 3.9 39.5 - - + +
856M GLU* 4.4 11.9 - - + -
864M GLY 5.6 0.9 - - - +
866M PRO* 6.2 0.7 - - + -
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Residues in contact with SER 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K ARG 2.6 24.3 + - - -
43K ILE* 3.7 0.9 + - - -
44K LEU 3.2 1.2 - - - -
45K LEU* 1.3 81.1 - - - +
47K SER* 1.3 71.9 + - - +
48K ILE 3.3 8.3 + - - +
148K VAL* 4.0 9.9 - - - +
149K GLY* 4.0 14.7 + - - -
172K SER* 4.1 9.2 + - - -
30L ARG* 5.6 7.4 + - - -
32L PHE* 4.9 3.9 - - - -
856M GLU* 4.0 22.9 + - - -
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Residues in contact with SER 47 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K ILE* 2.9 11.5 + - - -
46K SER* 1.3 78.9 + - - +
48K ILE* 1.3 59.4 + - - +
49K PRO* 3.2 13.9 - - - +
148K VAL* 3.5 15.2 - - - +
217K ILE* 3.6 28.5 - - - +
29L GLU* 5.5 1.4 - - - +
32L PHE* 3.1 36.2 - - - -
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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
------------------------------------------------------------
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