Contacts of the helix formed by residues 44 - 57 (chain K) in PDB entry 6L49
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 44 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178J G 3.4 2.9 + - - -
179J T 3.1 15.0 + - - -
42K ARG 3.1 1.4 + - - -
43K PRO* 1.3 74.4 - - - +
45K THR* 1.3 60.0 + - - +
47K ALA* 3.7 5.9 - - - +
48K LEU* 3.3 31.0 + - - +
44L LYS* 4.0 22.7 - - - +
115Q LEU 5.2 1.1 - - - +
117Q PRO* 5.4 9.6 - - - -
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Residues in contact with THR 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-100I G 3.7 28.7 + - - -
-99I A 3.3 25.8 - - - +
41K TYR* 3.8 9.9 - - + -
42K ARG* 3.4 21.7 - - + +
44K GLY* 1.3 74.3 - - - +
46K VAL* 1.3 63.1 + - - +
47K ALA 3.2 1.3 - - - -
48K LEU* 3.4 9.5 + - - +
49K ARG* 2.9 35.7 + - - +
52K ARG* 4.9 2.9 + - - -
117Q PRO* 5.3 10.4 - - - +
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Residues in contact with VAL 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179J T 3.1 27.0 + - + +
180J G 3.7 22.2 - - - +
41K TYR* 3.7 27.1 - - + -
42K ARG 4.5 0.2 + - - -
45K THR* 1.3 75.7 - - - +
47K ALA* 1.3 57.9 + - - +
49K ARG* 3.3 31.2 + - + +
50K GLU* 2.9 47.3 + - + +
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Residues in contact with ALA 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178J G 4.7 1.3 - - - +
179J T 2.6 20.4 + - - +
44K GLY* 3.7 11.4 - - - +
46K VAL* 1.3 74.3 - - - +
48K LEU* 1.3 57.3 + - + +
50K GLU* 3.3 2.3 + - - -
51K ILE* 2.9 34.1 + - + +
39L ARG* 3.4 40.2 - - - +
44L LYS* 4.3 16.6 - - + +
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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
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44K GLY 3.3 16.1 + - - +
45K THR* 3.8 8.1 - - - +
46K VAL 3.3 0.4 - - - -
47K ALA* 1.3 76.0 - - + +
49K ARG* 1.3 61.0 + - - +
51K ILE* 3.2 24.0 + - + +
52K ARG* 2.9 54.7 + - - +
44L LYS* 5.7 3.1 - - + -
111Q ILE* 3.8 25.3 - - + +
115Q LEU* 4.2 17.3 - - + +
116Q LEU* 3.9 17.3 - - + -
117Q PRO* 3.8 30.1 - - + -
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Residues in contact with ARG 49 (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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-100I G 5.6 1.2 - - - -
103J T 3.9 16.7 + - - -
104J G 3.7 39.4 + - - -
105J T 4.6 2.2 + - - +
180J G 5.0 1.0 + - - -
41K TYR* 3.3 46.8 + - - -
45K THR* 2.9 25.5 + - - +
46K VAL* 3.5 25.5 - - - +
47K ALA 3.3 0.2 - - - -
48K LEU* 1.3 77.5 - - - +
50K GLU* 1.3 57.2 + - + +
52K ARG* 3.4 18.1 + - + +
53K ARG* 2.9 28.6 + - - +
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Residues in contact with GLU 50 (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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179J T 5.0 1.9 + - - -
46K VAL* 2.9 34.6 + - + +
47K ALA* 3.6 4.7 - - - +
48K LEU 3.3 0.2 - - - -
49K ARG* 1.3 74.1 - - + +
51K ILE* 1.3 59.7 + - - +
53K ARG* 4.1 13.0 - - - +
54K TYR* 2.9 56.4 + - + +
35L ARG* 4.6 12.7 - - - +
36L ARG* 5.8 1.6 - - - +
39L ARG* 3.5 32.6 + - + +
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Residues in contact with ILE 51 (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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47K ALA 2.9 16.3 + - - +
48K LEU* 3.2 30.5 + - + +
50K GLU* 1.3 76.3 - - - +
52K ARG* 1.3 57.5 + - - +
54K TYR* 3.5 0.7 + - - +
55K GLN* 2.9 61.6 + - - +
39L ARG* 3.3 34.1 - - - +
42L GLY* 4.3 20.4 - - - -
43L VAL 4.5 5.4 - - - +
44L LYS* 5.2 3.8 - - - +
110Q ASN 4.4 1.8 - - - +
111Q ILE* 3.8 23.8 - - + -
115Q LEU* 5.6 3.6 - - + -
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Residues in contact with ARG 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-100I G 4.6 14.5 + - - -
105J T 5.7 0.7 - - - -
45K THR* 4.9 3.2 + - - -
48K LEU* 2.9 50.1 + - - +
49K ARG* 3.7 26.1 - - + +
51K ILE* 1.3 75.7 - - - +
53K ARG* 1.3 57.5 + - - +
55K GLN* 4.2 5.6 - - - +
56K LYS* 2.9 52.8 + - + +
111Q ILE* 4.3 20.7 - - + +
116Q LEU* 5.5 4.4 - - - +
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Residues in contact with ARG 53 (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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-184I A 5.7 3.8 + - - -
104J G 5.6 6.0 + - - -
105J T 3.3 52.7 + - - +
49K ARG 2.9 16.3 + - - +
50K GLU* 3.6 12.5 - - - +
51K ILE 3.3 0.4 - - - -
52K ARG* 1.3 77.5 - - - +
54K TYR* 1.3 96.6 + - + +
56K LYS* 4.0 1.5 - - - +
57K SER* 3.2 31.8 + - - -
59K GLU* 5.0 6.7 + - - -
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Residues in contact with TYR 54 (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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50K GLU* 2.9 41.5 + - + +
51K ILE 3.8 1.6 - - - +
53K ARG* 1.3 120.8 + - + +
55K GLN* 1.3 58.5 + - - +
57K SER* 3.5 8.2 - - - +
59K GLU* 3.7 18.6 - - + -
61K LEU* 3.7 14.1 - - + -
36L ARG* 3.3 46.0 - - + +
39L ARG* 3.8 15.3 - - + -
40L ARG* 3.1 50.8 + - + +
107Q VAL* 5.7 1.9 + - - +
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Residues in contact with GLN 55 (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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51K ILE* 2.9 38.1 + - + +
52K ARG* 4.2 5.1 + - - +
54K TYR* 1.3 80.3 - - - +
56K LYS* 1.3 62.7 + - + +
57K SER 3.5 3.9 - - - +
39L ARG 4.6 4.2 + - - +
40L ARG* 4.1 20.8 + - + +
42L GLY 5.1 3.2 - - - +
81Q ARG* 3.8 20.4 + - - -
107Q VAL* 4.0 15.5 - - + +
108Q LEU 3.9 5.3 + - - +
109Q PRO* 3.4 23.0 - - + +
110Q ASN* 3.0 52.8 + - - +
111Q ILE* 4.5 3.3 - - - +
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Residues in contact with LYS 56 (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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105J T 4.6 15.4 + - - +
106J A 3.4 39.1 + - - +
52K ARG* 2.9 34.6 + - - +
53K ARG* 4.0 3.6 - - - +
55K GLN* 1.3 79.8 - - - +
57K SER* 1.3 59.3 + - - +
58K THR* 5.3 0.9 - - - +
81Q ARG* 4.9 12.3 + - - +
109Q PRO* 5.6 5.2 - - + -
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Residues in contact with SER 57 (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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105J T 6.0 1.7 - - - -
106J A 5.3 2.9 + - - -
53K ARG* 3.2 16.2 + - - +
54K TYR* 3.5 17.7 - - - +
55K GLN 4.0 3.8 - - - +
56K LYS* 1.3 82.0 - - - +
58K THR* 1.3 67.8 + - - +
59K GLU* 3.7 18.4 - - - -
40L ARG* 4.3 3.0 + - - -
81Q ARG* 5.7 0.5 + - - -
106Q GLY* 5.3 2.6 - - - -
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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