Contacts of the helix formed by residues 38 - 54 (chain A) in PDB entry 4GEK
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A VAL 3.2 0.8 + - - -
37A PRO* 1.3 72.0 - - - +
39A TYR* 1.3 65.4 + - - +
40A SER* 3.3 3.4 - - - -
41A ASN* 3.0 16.1 + - - +
42A ILE* 3.0 26.8 + - - +
184A PHE* 4.9 2.8 - - - -
230A PHE* 3.7 23.1 - - - -
232A CYS* 4.5 5.0 - - - +
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Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 4.8 1.4 - - - -
32A ILE* 3.8 47.3 - - + +
33A GLN* 5.3 7.6 - - + -
36A VAL* 3.1 27.5 + - + +
37A PRO 3.3 1.2 + - - -
38A GLY* 1.3 76.3 - - - +
40A SER* 1.3 69.8 + - - +
42A ILE* 3.2 9.6 + - - +
43A ILE* 2.9 38.2 + - + +
69A ALA* 3.1 20.6 - - + +
132A ASN* 3.8 15.0 - - - -
133A PHE* 4.1 19.5 - + - -
302A GEK 2.6 31.0 + - + -
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Residues in contact with SER 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 5.8 7.4 - - - -
38A GLY* 5.1 0.9 - - - -
39A TYR* 1.3 87.5 - - - +
41A ASN* 1.4 64.9 + - - +
43A ILE* 3.3 7.7 + - - +
44A SER* 3.0 28.2 + - - -
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Residues in contact with ASN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY* 3.0 15.7 + - - +
40A SER* 1.4 87.8 + - - +
42A ILE* 1.3 57.9 + - - +
44A SER* 3.2 8.5 + - - -
45A MET* 2.9 35.2 + - - +
230A PHE* 3.6 30.3 - - + -
38G GLY* 5.8 0.8 - - - -
41G ASN* 2.8 30.0 + - - +
230G PHE* 4.9 0.6 - - - -
232G CYS* 5.6 3.7 - - - -
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO 5.0 1.8 - - - +
38A GLY 3.0 17.2 + - - +
39A TYR* 3.6 6.1 - - - +
41A ASN* 1.3 75.5 - - - +
43A ILE* 1.3 56.6 + - - +
45A MET* 3.1 9.4 + - + +
46A ILE* 2.8 37.7 + - + +
132A ASN* 3.4 25.4 - - - +
133A PHE* 3.7 30.1 - - + -
161A VAL* 5.1 0.2 - - + -
163A SER* 3.5 8.7 - - - +
229A TRP* 5.5 1.3 - - + +
230A PHE* 3.5 38.4 - - + -
235A PHE* 5.7 0.4 - - + -
236A GLY* 4.4 4.5 - - - +
237A SER* 4.2 15.7 - - - +
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 2.9 47.8 + - + +
40A SER* 3.3 9.6 + - - +
42A ILE* 1.3 75.5 - - - +
44A SER* 1.3 62.2 + - - +
46A ILE* 3.3 6.5 + - + +
47A GLY 3.2 7.1 + - - -
69A ALA* 4.0 9.0 - - + +
70A ALA* 3.9 27.8 - - + +
73A SER* 2.7 42.0 + - - +
76A ARG* 4.6 8.3 - - - +
132A ASN* 3.7 23.3 - - - +
302A GEK 4.0 0.2 - - - +
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER 3.0 12.4 + - - -
41A ASN* 3.2 12.5 + - - -
43A ILE* 1.3 78.4 - - - +
45A MET* 1.3 57.8 + - - +
47A GLY* 3.2 4.0 + - - -
48A MET* 3.0 39.0 + - - +
73A SER* 4.6 2.0 - - - -
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Residues in contact with MET 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN* 2.9 21.7 + - + +
42A ILE* 3.1 9.2 + - - +
44A SER* 1.3 75.6 - - - +
46A ILE* 1.3 60.0 + - - +
48A MET* 3.1 10.3 + - - +
49A LEU 2.9 25.5 + - - -
229A TRP* 3.3 60.6 - - + +
230A PHE* 3.5 31.9 - - + -
232G CYS* 4.1 9.4 - - - -
233G PHE* 3.6 42.0 - - + +
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 2.8 22.6 + - + +
43A ILE* 3.4 11.2 - - + +
45A MET* 1.3 76.1 - - - +
47A GLY* 1.3 56.9 + - - +
49A LEU* 3.3 3.6 + - - -
50A ALA* 2.9 26.7 + - - +
70A ALA* 4.3 14.6 - - + +
73A SER* 4.5 2.5 - - - +
74A VAL* 3.6 26.5 - - + -
128A MET* 3.5 12.5 - - + +
130A VAL* 4.1 18.8 - - + -
132A ASN* 3.7 34.3 - - + +
161A VAL* 4.0 23.6 - - + -
229A TRP* 4.3 2.4 - - + -
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Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE 3.2 11.7 + - - -
44A SER 3.2 3.5 + - - -
46A ILE* 1.3 75.6 - - - +
48A MET* 1.3 62.6 + - - +
50A ALA* 3.2 2.2 + - - -
51A GLU* 3.1 18.0 + - - +
73A SER* 3.3 21.9 + - - -
77A ASN* 3.2 32.6 - - - +
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Residues in contact with MET 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER* 3.0 26.4 + - - +
45A MET* 3.1 9.8 + - - +
47A GLY* 1.3 74.8 - - - +
49A LEU* 1.3 63.2 + - - +
51A GLU* 3.3 19.3 + - - +
52A ARG* 3.6 4.3 + - - +
77A ASN* 5.1 1.8 - - - -
180G MET* 3.5 44.0 - - + +
183G ASP* 3.8 16.8 - - + +
184G PHE* 3.6 23.8 - - - +
187G ALA* 5.9 1.1 - - + -
233G PHE* 3.7 28.0 - - + -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A MET 2.9 16.3 + - - +
46A ILE 3.6 4.9 - - - +
48A MET* 1.3 75.6 - - - +
50A ALA* 1.3 59.4 + - - +
52A ARG 3.0 3.1 + - - -
53A PHE* 2.8 61.4 + - + +
128A MET* 4.1 8.7 - - + -
159A ALA* 4.0 20.0 - - + -
161A VAL* 3.5 31.0 - - + -
229A TRP* 3.8 19.7 - - + -
239A VAL* 4.0 7.0 - - + -
176G LEU* 3.8 20.9 - - + -
180G MET* 4.2 6.9 - - + -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE 2.9 14.7 + - - +
47A GLY 3.2 8.9 + - - +
49A LEU* 1.3 77.6 - - - +
51A GLU* 1.4 61.9 + - - +
53A PHE 4.4 0.4 - - - +
54A VAL* 3.0 42.1 + - + +
74A VAL* 3.9 32.3 - - + +
77A ASN* 4.1 6.6 - - + +
128A MET* 3.8 14.6 - - - -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLY 3.1 10.9 + - - +
48A MET* 3.5 13.1 - - - +
49A LEU 3.2 0.2 - - - -
50A ALA* 1.4 76.2 - - - +
52A ARG* 1.3 64.0 + - + +
54A VAL 5.0 3.6 - - - +
77A ASN* 3.0 32.1 + - - +
79A HIS* 2.9 34.2 + - + -
80A HIS* 5.0 6.8 + - - -
183G ASP* 5.9 1.6 - - - +
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Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A MET 3.6 4.8 + - - +
49A LEU 3.0 3.7 + - - +
51A GLU* 1.3 83.9 - - + +
53A PHE* 1.3 80.6 + - + +
54A VAL 3.9 1.6 - - - -
55A GLN* 4.2 10.2 + - - -
176G LEU* 5.7 0.9 - - - -
179G ASN* 3.7 39.1 + - - +
180G MET* 3.8 15.0 - - + -
182G HIS* 3.8 14.5 + - - -
183G ASP* 2.7 43.3 + - - +
186G ARG* 4.8 3.0 - - - +
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Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 2.8 34.7 + - + +
52A ARG* 1.3 95.3 - - + +
54A VAL* 1.3 64.5 + - - +
55A GLN* 3.2 15.9 + - - +
127A SER* 3.5 19.9 - - - +
128A MET* 4.9 4.9 - - - -
157A GLY 3.4 28.3 - - - +
158A GLY* 5.5 0.2 - - - -
159A ALA* 3.8 21.1 - - + -
241A LEU* 3.8 27.1 - - + -
172G LYS* 5.8 6.3 - - - -
176G LEU* 3.6 31.6 - - + -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 3.0 36.6 + - + +
51A GLU 5.0 1.7 - - - +
52A ARG 5.1 1.0 - - - -
53A PHE* 1.3 76.3 + - - +
55A GLN* 1.3 64.7 + - - +
58A THR* 4.3 0.9 - - - +
60A VAL* 3.7 28.0 - - + -
74A VAL* 4.3 1.3 - - + -
78A ILE* 3.9 29.4 - - + -
80A HIS* 3.1 23.8 + - + -
83A CYS* 3.9 18.6 - - + -
127A SER* 3.4 11.4 - - - +
128A MET* 4.2 8.7 - - + -
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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
------------------------------------------------------------
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