Contacts of the helix formed by residues 35 - 48 (chain K) in PDB entry 6XAV
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 PHE 35 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46H ILE* 4.1 25.6 - - + -
50H SER* 3.5 28.0 - - - -
223H ILE* 4.1 21.8 - - + -
224H LEU* 4.9 1.8 - - + -
227H GLN* 3.7 33.4 - - + -
8K PHE* 3.9 17.7 - + - -
31K LEU* 4.1 7.2 - - + +
32K GLU* 3.5 28.4 + - + +
33K ARG 3.2 18.9 - - - -
34K GLY* 1.3 80.4 - - - +
36K GLY* 1.3 60.9 + - - +
37K HIS 3.5 0.7 - - - -
38K THR* 3.8 8.7 - - + -
39K LEU* 3.0 46.9 + - + +
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Residues in contact with GLY 36 (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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31K LEU* 3.7 21.1 - - - +
32K GLU 4.4 3.6 + - - -
34K GLY 3.7 1.0 - - - +
35K PHE* 1.3 77.6 - - - +
37K HIS* 1.3 53.1 + - - +
39K LEU* 4.3 0.5 - - - +
40K GLY* 2.7 33.4 + - - -
187K VAL* 3.5 31.1 - - - +
199K ASP* 6.0 0.4 - - - +
201K LEU* 3.9 3.5 - - - +
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Residues in contact with HIS 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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41H ASN* 5.8 0.2 + - - -
45H ARG* 3.5 27.7 + - - +
1213I TYR* 5.1 17.3 - + - -
1217I THR 4.8 1.0 - - - +
1218I GLY* 3.5 26.2 + - - +
1219I GLU* 5.9 0.4 - - - -
1220I GLN* 6.3 2.0 - - + -
34K GLY* 6.0 2.7 - - - -
36K GLY* 1.3 74.7 - - - +
38K THR* 1.3 65.2 + - - +
40K GLY 4.4 0.4 - - - +
41K ASN* 3.2 27.0 + - - +
185K TYR* 4.4 12.3 - + - -
187K VAL* 4.0 30.3 - - + +
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Residues in contact with THR 38 (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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41H ASN* 5.8 1.4 + - - +
42H ALA* 3.8 32.1 - - + +
45H ARG* 3.0 27.6 + - + +
46H ILE* 3.9 20.5 - - + +
224H LEU* 4.7 8.9 - - + +
34K GLY 2.4 28.0 + - - -
35K PHE* 3.6 11.8 + - + -
36K GLY 3.2 0.4 - - - -
37K HIS* 1.3 80.4 - - - +
39K LEU* 1.3 57.2 + - + +
41K ASN* 4.9 0.5 - - - +
42K ALA* 3.3 22.7 + - - +
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Residues in contact with LEU 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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224H LEU* 3.7 29.4 - - + -
227H GLN* 4.4 19.5 - - + +
228H LEU* 4.1 22.4 - - + -
231H PHE* 6.3 0.2 - - + -
11K PRO* 4.6 8.7 - - + -
28K LEU* 5.8 5.4 - - + -
31K LEU* 4.2 22.4 - - + -
35K PHE* 3.0 29.7 + - + +
36K GLY 4.3 0.4 - - - +
38K THR* 1.3 79.0 - - - +
40K GLY* 1.3 64.8 + - - +
41K ASN 3.4 0.4 - - - -
42K ALA* 3.8 2.3 - - + +
43K LEU* 3.0 35.2 + - + +
201K LEU* 4.3 11.2 - - + -
224K LEU* 5.2 6.5 - - + -
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Residues in contact with GLY 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 GLY 2.7 22.3 + - - -
39K LEU* 1.3 73.7 - - - +
41K ASN* 1.3 60.4 + - - +
43K LEU* 4.1 2.8 - - - +
44K ARG* 3.1 17.3 + - - +
183K ILE* 5.6 0.2 - - - +
185K TYR* 3.4 35.6 - - - -
201K LEU* 3.7 13.8 - - - +
203K ILE* 5.5 1.8 - - - +
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Residues in contact with ASN 41 (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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41H ASN* 4.8 3.7 + - - +
1087I TYR* 3.3 16.8 + - - -
1215I GLY* 3.0 24.2 + - - +
1216I ARG 3.5 9.9 - - - +
1217I THR 4.0 2.4 - - - -
1218I GLY* 3.3 26.7 - - - +
37K HIS 3.2 17.7 + - - +
38K THR 4.9 0.7 - - - +
40K GLY* 1.3 73.7 - - - +
42K ALA* 1.3 61.8 + - - +
44K ARG* 3.1 4.0 + - - +
45K ARG* 2.9 49.1 + - - +
185K TYR* 3.3 17.8 - - - +
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Residues in contact with ALA 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H THR* 4.2 18.6 - - + +
42H ALA* 5.0 11.4 - - + -
224H LEU* 6.3 0.7 - - + -
38K THR 3.3 20.6 + - - +
39K LEU* 3.4 6.9 + - + +
40K GLY 3.4 0.4 - - - -
41K ASN* 1.3 82.3 + - - +
43K LEU* 1.3 61.1 + - - +
45K ARG* 3.7 4.2 + - - +
46K ILE* 3.3 25.9 - - - +
224K LEU* 4.0 22.0 - - + -
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Residues in contact with LEU 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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228H LEU* 5.1 9.0 - - + -
231H PHE* 6.1 0.9 - - + -
28K LEU* 3.9 27.8 - - + -
39K LEU* 3.0 26.9 + - + +
40K GLY 4.1 2.7 - - - +
42K ALA* 1.3 78.4 - - + +
44K ARG* 1.3 60.7 + - - +
46K ILE* 3.2 5.2 + - + +
47K LEU* 3.0 40.7 + - + +
183K ILE* 6.4 0.2 - - + -
201K LEU* 4.9 0.7 - - + -
203K ILE* 4.1 19.1 - - + -
217K ILE* 4.6 13.2 - - + +
220K ALA* 4.4 8.0 - - + +
221K ALA* 4.1 34.5 - - + +
224K LEU* 4.6 11.9 - - + -
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Residues in contact with ARG 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082I ILE 4.0 5.1 + - - -
1083I GLU* 3.9 17.0 + - - +
1085I MET 4.2 1.0 + - - -
1087I TYR* 3.3 51.6 - - - +
1091I GLY 3.3 21.0 + - - -
1093I PRO* 3.7 14.3 - - - +
1215I GLY 5.2 0.6 + - - -
40K GLY 3.1 18.2 + - - +
41K ASN* 3.1 5.1 + - - +
43K LEU* 1.3 79.0 - - - +
45K ARG* 1.3 61.7 + - + +
46K ILE 3.2 1.0 + - - -
47K LEU* 4.6 0.9 - - - +
48K LEU* 3.3 49.2 + - + +
183K ILE* 3.1 47.4 + - + +
185K TYR* 3.8 15.7 - - + -
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Residues in contact with ARG 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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34H GLY* 2.4 29.4 + - - -
35H PHE* 4.6 3.6 - - - -
37H HIS* 3.8 10.7 - - - +
38H THR* 2.4 44.0 + - + +
1083I GLU* 3.3 34.2 + - + +
1084I ASP* 3.0 37.9 + - - -
1215I GLY 3.0 25.9 + - - +
1216I ARG* 3.4 10.9 - - - +
41K ASN* 2.9 35.0 + - - +
42K ALA 4.1 6.1 - - - +
43K LEU 3.2 0.4 - - - -
44K ARG* 1.3 77.2 - - + +
46K ILE* 1.3 53.1 + - - +
49K SER* 2.7 31.0 + - - -
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Residues in contact with ILE 46 (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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35H PHE* 4.0 18.2 - - + -
38H THR* 4.8 3.6 - - + -
42K ALA 3.3 17.9 - - - +
43K LEU* 3.2 6.8 + - + +
44K ARG 3.1 0.2 - - - -
45K ARG* 1.3 79.4 - - - +
47K LEU* 1.3 65.1 + - - +
48K LEU 3.2 1.6 - - - -
49K SER* 3.3 4.3 - - - +
50K SER* 3.1 44.2 + - - +
220K ALA* 3.6 41.3 - - + +
223K ILE* 4.2 17.0 - - + -
224K LEU* 3.6 33.4 - - + +
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Residues in contact with LEU 47 (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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43K LEU* 3.0 27.8 + - + +
44K ARG 4.2 0.4 - - - +
46K ILE* 1.3 76.5 - - - +
48K LEU* 1.3 60.5 + - - +
51K MET* 3.1 28.8 - - + +
178K SER* 5.4 0.5 + - - -
180K VAL* 3.3 20.9 - - + +
183K ILE* 3.6 42.4 - - + -
203K ILE* 5.0 5.6 - - + -
205K MET* 4.5 13.9 - - + -
216K ALA* 3.2 41.7 - - + +
217K ILE* 4.6 7.4 - - + +
220K ALA* 3.7 11.9 - - + -
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Residues in contact with LEU 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821I ARG* 4.4 6.5 - - - +
1082I ILE* 4.0 36.8 - - + +
1083I GLU* 4.3 9.6 - - + -
1093I PRO* 5.1 0.7 - - + -
44K ARG* 3.3 58.3 + - + +
46K ILE 3.2 0.2 - - - -
47K LEU* 1.3 78.8 - - - +
49K SER* 1.3 66.1 + - - +
178K SER* 4.3 12.3 + - - -
180K VAL* 3.7 24.6 - - + +
181K GLU 4.0 7.9 - - - +
182K ARG* 4.0 14.8 - - - -
183K ILE* 3.8 13.2 - - + +
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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