Contacts of the helix formed by residues 48 - 60 (chain A) in PDB entry 1SEK
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.6 15.5 - - + -
23A ASN* 3.3 30.6 + - + +
27A THR* 4.7 0.4 + - - -
47A ALA* 1.3 80.4 - - - +
49A SER* 1.3 62.6 + - - +
50A VAL 3.1 0.4 + - - -
51A LEU* 3.4 9.6 + - + +
52A PRO* 3.2 20.1 - - + +
88A LEU* 4.0 32.3 - - + -
92A VAL* 6.4 1.6 - - + -
102A MET* 4.0 15.0 - - + -
373A TYR* 6.3 0.7 - + - -
376A ASN* 4.1 18.2 - - + -
377A SER 3.8 13.2 + - - +
378A MET* 3.7 48.0 - - + +
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Residues in contact with SER 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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46A SER* 3.2 24.4 + - - -
48A PHE* 1.3 78.5 - - - +
50A VAL* 1.3 58.9 + - - +
52A PRO* 3.6 6.8 - - - +
53A PRO* 3.5 11.6 - - - +
102A MET* 3.8 35.2 - - - -
103A ALA 5.9 0.2 - - - -
104A SER* 3.6 3.3 + - - -
176A ASN* 2.9 38.4 + - - +
177A ALA 5.3 0.2 - - - -
178A ILE* 4.3 5.0 - - - +
329A GLN* 3.4 1.7 + - - -
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Residues in contact with VAL 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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26A PHE* 4.4 9.9 - - + -
30A MET* 4.2 11.0 - - + -
46A SER 3.4 6.3 - - - +
47A ALA* 3.5 10.3 - - - +
48A PHE 3.1 0.6 - - - -
49A SER* 1.3 77.8 - - - +
51A LEU* 1.3 62.0 + - - +
53A PRO* 2.8 21.4 - - + +
54A LEU* 3.2 34.5 + - + +
174A LEU* 6.0 3.4 - - + -
176A ASN* 3.7 9.6 - - - +
292A LEU* 4.4 13.7 - - + -
296A LEU* 4.9 11.9 - - + -
329A GLN* 3.2 29.4 - - - +
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Residues in contact with LEU 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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19A LEU* 4.5 15.7 - - + -
22A SER* 4.8 6.3 - - - +
23A ASN* 3.8 39.5 - - + +
26A PHE* 3.8 32.1 - - + -
47A ALA 3.1 15.4 + - - +
48A PHE* 3.7 8.3 - - + +
50A VAL* 1.3 76.9 - - - +
52A PRO* 1.3 64.4 - - + +
54A LEU* 3.1 6.2 + - + +
55A GLY* 2.8 24.9 + - - -
73A LEU* 3.9 20.1 - - + +
85A PHE* 3.7 21.2 - - + -
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Residues in contact with PRO 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 PHE* 3.2 17.0 - - + +
49A SER* 3.6 6.3 - - - +
50A VAL 3.5 0.7 - - - -
51A LEU* 1.3 90.1 - - + +
53A PRO* 1.3 65.7 - - + +
55A GLY 2.9 2.3 + - - -
56A GLN* 2.9 25.1 + - - +
85A PHE* 3.7 24.7 - - + -
88A LEU* 4.8 11.0 - - + -
104A SER* 5.8 1.6 - - - -
126A PHE* 3.3 34.0 - - + +
128A SER* 5.2 1.8 - - - -
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Residues in contact with PRO 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 SER 3.5 4.7 - - - +
50A VAL* 2.8 25.6 - - + +
52A PRO* 1.3 95.4 - - + +
54A LEU* 1.3 56.1 + - - +
56A GLN* 3.4 21.9 + - - +
57A LEU* 2.9 33.6 + - - +
104A SER* 2.8 32.5 - - - +
128A SER* 4.2 2.7 - - - +
174A LEU* 3.9 29.6 - - + -
176A ASN* 4.5 1.6 - - + +
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Residues in contact with LEU 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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26A PHE* 3.7 31.4 - - + -
50A VAL* 3.2 26.9 + - + +
51A LEU 3.1 9.0 + - - +
53A PRO* 1.3 78.7 - - + +
55A GLY* 1.3 58.8 + - - +
57A LEU* 3.4 9.5 + - + +
58A ALA* 3.0 26.5 + - - +
69A LEU* 3.5 26.0 - - + +
73A LEU* 3.9 22.4 - - + +
174A LEU* 5.2 5.4 - - + -
296A LEU* 4.3 18.2 - - + -
301A ILE* 4.2 11.7 - - + -
304A LEU* 4.5 12.6 - - + -
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Residues in contact with GLY 55 (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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51A LEU 2.8 13.3 + - - -
52A PRO 2.9 3.6 + - - -
54A LEU* 1.3 77.6 - - - +
56A GLN* 1.3 63.1 + - - +
58A ALA* 3.3 4.5 + - - +
59A LEU* 3.2 17.0 + - - +
73A LEU* 4.0 13.6 - - - +
81A THR* 3.9 11.0 - - - +
85A PHE* 4.1 2.9 - - - -
126A PHE* 3.3 23.8 - - - -
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Residues in contact with GLN 56 (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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52A PRO 2.9 12.4 + - - +
53A PRO* 3.5 14.5 - - - +
55A GLY* 1.3 76.7 - - - +
57A LEU* 1.3 62.4 + - - +
59A LEU* 3.4 2.0 + - - +
60A ALA 3.3 7.1 + - - -
106A ILE* 3.2 28.9 - - + +
118A PHE* 3.1 38.9 - - + -
122A SER* 2.8 21.8 + - - +
126A PHE* 3.5 28.6 - - + -
128A SER* 3.1 37.9 + - - +
129A GLU 4.3 0.2 - - - +
130A VAL* 3.5 12.1 - - - +
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Residues in contact with LEU 57 (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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53A PRO 2.9 19.3 + - - +
54A LEU* 3.7 9.6 - - + +
55A GLY 3.2 0.2 - - - -
56A GLN* 1.3 79.3 - - + +
58A ALA* 1.3 57.6 + - - +
60A ALA* 3.2 6.4 + - + +
61A SER* 2.5 34.5 + - - -
69A LEU* 4.0 9.6 - - + -
106A ILE* 3.5 30.7 - - + -
118A PHE* 5.5 0.4 - - + -
174A LEU* 4.3 22.0 - - + -
304A LEU* 3.7 35.2 - - + -
312A LEU* 3.8 17.4 - - + +
315A LEU* 4.9 7.9 - - + -
324A VAL* 4.7 9.0 - - + -
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Residues in contact with ALA 58 (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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54A LEU 3.0 17.5 + - - +
55A GLY* 3.3 9.8 + - - +
57A LEU* 1.3 76.7 - - - +
59A LEU* 1.3 63.0 + - - +
60A ALA 3.5 0.2 + - - -
61A SER* 3.6 5.2 + - - +
66A HIS* 2.8 32.5 + - + -
69A LEU* 4.0 22.2 - - + +
70A LEU* 4.0 26.9 - - + -
73A LEU* 4.9 2.0 - - + -
78A ASP* 5.1 0.4 - - - +
81A THR* 5.1 2.2 - - + -
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Residues in contact with LEU 59 (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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55A GLY 3.2 13.6 + - - +
56A GLN* 3.6 10.1 - - - +
57A LEU 3.2 0.4 - - - -
58A ALA* 1.3 77.1 - - + +
60A ALA* 1.3 58.2 + - - +
61A SER 3.4 2.1 + - - +
78A ASP* 3.7 48.2 - - + +
81A THR* 4.2 10.3 - - + -
82A LYS* 3.2 29.6 - - + +
118A PHE* 4.1 8.9 - - + -
121A VAL* 4.8 11.4 - - + -
126A PHE* 3.5 23.8 - - + -
314A ASN* 3.3 19.6 + - - +
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Residues in contact with ALA 60 (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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56A GLN 3.3 2.1 + - - +
57A LEU* 3.2 11.5 + - + +
59A LEU* 1.3 80.0 - - - +
61A SER* 1.3 57.5 + - - +
118A PHE* 3.3 31.6 - - + -
312A LEU* 3.2 21.0 - - + -
313A GLU 3.3 0.9 + - - -
314A ASN* 3.1 31.6 + - - +
315A LEU* 4.2 16.8 - - + +
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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