Contacts of the helix formed by residues 16 - 28 (chain k) in PDB entry 5GJQ
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 LEU 16 (chain k).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8k THR* 4.1 6.3 - - + -
9k VAL 3.5 22.4 - - - +
10k PHE* 3.5 31.2 - - + -
14k GLY 5.6 0.4 - - - +
15k HIS* 1.3 69.0 - - - +
17k PHE* 1.3 67.2 + - - +
18k GLN 3.3 2.2 - - - -
19k VAL* 3.1 37.3 + - + +
20k GLU* 3.3 16.5 + - + +
119k THR* 5.3 2.5 - - - -
81l LEU* 4.1 17.0 - - + -
84l ASP* 5.2 0.9 - - - +
135l ARG* 3.9 40.2 - - - +
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Residues in contact with PHE 17 (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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424H SER* 6.0 0.7 - - - -
427H PRO* 4.3 24.0 - - + -
8k THR* 5.6 0.4 - - - +
9k VAL 4.4 4.8 + - - -
11k SER* 3.6 31.4 - - - -
13k ASP* 4.4 4.5 - - - -
15k HIS* 3.7 16.6 + + + -
16k LEU* 1.3 73.9 - - - +
18k GLN* 1.3 66.4 + - + +
20k GLU* 3.1 27.1 + - - +
21k TYR* 2.9 63.4 + + + +
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Residues in contact with GLN 18 (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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11j ILE* 2.7 36.6 - - + +
12j PHE* 2.9 46.2 + - - +
7k ILE* 3.9 27.1 - - + +
8k THR* 3.9 19.7 - - - +
16k LEU 3.3 0.4 - - - -
17k PHE* 1.3 78.5 - - + +
19k VAL* 1.3 58.1 + - - +
21k TYR* 3.4 14.4 + - - +
22k ALA* 2.9 27.2 + - - +
126k PRO* 4.2 12.8 - - + +
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Residues in contact with VAL 19 (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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8k THR* 4.1 15.7 - - + -
16k LEU* 3.1 35.4 + - + +
18k GLN* 1.3 75.3 - - - +
20k GLU* 1.3 62.7 + - + +
22k ALA* 3.3 7.3 - - - +
23k GLN* 3.0 35.2 + - - +
119k THR* 4.2 15.7 - - + -
126k PRO* 4.5 5.6 - - + -
149k PRO* 3.8 11.0 - - + +
150k SER* 3.8 35.9 - - - +
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Residues in contact with GLU 20 (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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421H ALA* 6.0 2.3 - - - +
15k HIS* 3.2 35.4 + - - +
16k LEU 3.6 11.3 + - - +
17k PHE* 3.1 30.7 + - - +
19k VAL* 1.3 80.0 - - + +
21k TYR* 1.3 63.8 + - + +
23k GLN* 3.1 20.5 + - - +
24k GLU* 3.0 28.2 + - - +
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Residues in contact with TYR 21 (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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422H LYS* 6.4 2.2 - - + -
12j PHE* 3.9 23.8 - - + -
13j SER 3.7 13.9 - - - +
14j PRO* 3.6 51.4 - - + +
16j GLY* 3.6 7.3 - - - -
17k PHE* 2.9 60.2 + + + +
18k GLN* 3.9 13.2 - - - +
20k GLU* 1.3 80.3 - - + +
22k ALA* 1.3 66.1 + - - +
24k GLU* 3.1 12.0 + - + +
25k ALA* 3.0 17.8 + - - +
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Residues in contact with ALA 22 (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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12j PHE* 4.3 14.5 - - + -
18k GLN 2.9 14.5 + - - +
19k VAL* 3.3 12.8 - - - +
21k TYR* 1.3 79.1 - - - +
23k GLN* 1.3 62.3 + - - +
25k ALA* 3.0 19.0 + - - +
26k VAL* 3.0 16.8 + - - +
126k PRO* 4.5 5.6 - - + -
127k PHE 4.1 2.2 - - - +
128k GLY* 4.0 14.3 - - - -
149k PRO* 3.9 17.5 - - + -
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Residues in contact with GLN 23 (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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19k VAL* 3.0 25.8 + - - +
20k GLU* 3.1 22.1 + - - +
22k ALA* 1.3 73.7 - - - +
24k GLU* 1.3 60.2 + - - +
26k VAL* 3.2 11.0 + - + +
27k LYS* 2.9 25.7 + - - +
148k ASP* 3.0 37.4 + - - +
149k PRO* 3.9 12.6 - - + -
150k SER* 4.8 4.0 + - - -
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Residues in contact with GLU 24 (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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422H LYS* 4.7 20.2 - - - +
14j PRO 3.8 16.7 - - - +
15j GLU* 3.5 15.7 - - - +
16j GLY* 3.9 11.0 - - - -
20k GLU 3.0 16.7 + - - +
21k TYR* 3.1 13.7 - - + +
23k GLN* 1.3 75.1 - - - +
25k ALA* 1.3 61.9 + - - +
27k LYS* 2.8 28.8 + - - +
28k LYS* 3.0 24.8 + - - +
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Residues in contact with ALA 25 (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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12j PHE* 3.7 24.7 - - + -
16j GLY* 3.6 25.1 - - - +
21k TYR 3.0 2.3 + - - +
22k ALA 3.0 10.9 + - - +
24k GLU* 1.3 80.4 - - - +
26k VAL* 1.3 60.9 + - - +
28k LYS* 3.3 18.3 + - - +
29k GLY 3.7 3.6 + - - -
75k GLY* 3.9 12.0 - - - +
76k LEU* 4.3 10.5 - - + +
128k GLY 4.3 7.6 - - - +
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Residues in contact with VAL 26 (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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22k ALA 3.0 13.4 + - - +
23k GLN* 3.4 8.3 - - - +
25k ALA* 1.3 78.1 - - - +
27k LYS* 1.3 53.8 + - - +
28k LYS 3.0 0.2 - - - -
29k GLY* 2.7 27.2 + - - -
74k ALA* 3.5 19.7 - - + +
75k GLY* 3.9 5.8 - - - -
128k GLY 3.6 17.3 - - - +
129k ILE 3.6 10.8 - - - -
130k SER* 3.3 32.1 - - - +
149k PRO* 3.8 9.2 - - + -
161k ILE* 5.1 2.9 - - + -
162k GLY* 3.8 13.5 - - - +
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Residues in contact with LYS 27 (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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23k GLN 2.9 12.7 + - - +
24k GLU* 2.8 22.9 + - - +
26k VAL* 1.3 76.5 - - - +
28k LYS* 1.3 59.7 + - + +
29k GLY 3.2 1.2 + - - -
162k GLY 3.8 8.0 - - - +
163k ARG* 3.6 21.6 + - - +
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Residues in contact with LYS 28 (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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15j GLU* 2.3 58.8 + - - +
16j GLY 4.7 8.0 - - - +
17j ARG* 5.2 2.0 - - - +
24k GLU* 3.0 18.7 + - - +
25k ALA* 3.7 10.3 - - - +
26k VAL 3.0 1.8 - - - -
27k LYS* 1.3 79.1 - - + +
29k GLY* 1.3 62.5 + - - +
163k ARG* 5.2 3.3 - - - +
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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