Contacts of the strand formed by residues 37 - 44 (chain B) in PDB entry 1EKF
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 HIS 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B GLU 4.1 12.6 - - - -
14B MET* 3.8 19.9 - - + +
15B THR* 2.9 42.1 + - + -
35B THR* 3.5 16.8 + - - +
36B ASP* 1.3 97.1 - - + +
38B MET* 1.3 63.7 + - - +
53B ILE* 3.9 12.3 - - + -
54B GLN 3.2 15.0 - - - +
55B PRO 4.4 0.7 - - - -
56B PHE* 3.9 7.5 - - - +
124B LEU* 3.9 17.3 - - + +
127B VAL* 4.1 13.7 - - + +
128B ASP* 3.0 23.9 + - - +
165B VAL 4.8 0.5 - - - +
167B LEU* 4.9 4.3 + - - +
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Residues in contact with MET 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PRO* 3.8 30.5 - - + -
37B HIS* 1.3 76.4 - - - +
39B LEU* 1.3 62.4 + - - +
40B MET* 3.9 23.3 - - + -
52B ARG 3.5 0.7 - - - +
53B ILE* 3.3 3.6 - - - -
54B GLN* 2.8 49.0 + - + +
55B PRO 3.8 4.9 - - - +
56B PHE* 3.9 5.6 - - + -
57B GLN* 3.5 38.1 - - - +
59B LEU* 4.6 1.6 - - + -
124B LEU* 3.6 8.9 - - - +
164B PHE* 4.2 13.0 - - + -
165B VAL 3.3 15.0 - - - +
166B ILE* 4.1 13.0 - - + -
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 4.2 7.6 - - + -
38B MET* 1.3 75.7 - - - +
40B MET* 1.3 63.7 + - - +
41B VAL* 4.3 16.2 - - + -
51B PRO* 4.6 0.2 - - + -
52B ARG 3.2 28.3 - - - +
53B ILE* 4.2 7.9 - - + +
117B LEU* 3.9 15.3 - - + -
120B CYS* 3.7 39.3 - - + +
121B ILE* 4.6 2.0 - - + -
124B LEU* 4.0 9.3 - - + +
163B LEU* 4.7 2.0 - - + -
164B PHE* 3.0 26.2 - - - +
165B VAL* 3.0 40.9 + - + +
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Residues in contact with MET 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B MET* 3.9 16.4 - - + -
39B LEU* 1.3 75.8 - - - +
41B VAL* 1.3 62.4 + - - +
42B GLU* 4.8 4.5 - - + +
50B GLN 4.1 1.4 - - - +
51B PRO* 3.8 0.7 - - - +
52B ARG* 2.8 71.6 + - - +
54B GLN* 3.7 18.4 - - + +
57B GLN* 6.0 0.9 - - + -
58B ASN 6.0 0.2 - - - +
59B LEU* 3.5 29.6 - - + -
162B LEU* 3.3 38.8 - - + -
163B LEU 3.5 2.7 - - - -
164B PHE* 4.1 3.8 - - + -
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 4.3 25.6 - - + -
39B LEU* 4.3 14.8 - - + -
40B MET* 1.3 80.5 - - - +
42B GLU* 1.3 64.9 + - - +
48B TRP* 3.6 27.2 - - + -
49B GLY 3.8 20.2 - - - +
50B GLN 4.3 2.9 - - - +
51B PRO* 3.9 23.3 - - + -
52B ARG* 5.9 0.4 - - - +
162B LEU* 3.4 2.8 - - - +
163B LEU* 2.8 46.8 + - + +
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B MET* 4.8 4.6 - - + +
41B VAL* 1.3 76.5 - - - +
43B TRP* 1.3 61.6 + - - +
44B ASN* 6.1 2.5 - - - +
47B GLY 4.0 0.2 - - - +
48B TRP* 3.5 5.1 - - - -
49B GLY* 2.8 34.5 + - - +
50B GLN 5.1 1.4 + - - -
52B ARG* 4.3 19.4 + - - +
149B ASN* 5.2 2.1 + - - -
160B ARG* 4.3 21.2 + - + +
161B ALA 3.8 6.4 - - - +
162B LEU* 3.4 23.4 - - + +
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Residues in contact with TRP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 1.3 75.8 - - - +
44B ASN* 1.3 73.3 + - - +
45B ASP* 5.8 1.1 - - - -
47B GLY* 3.4 32.6 - - - -
48B TRP* 3.5 38.5 - + + -
110B PRO* 3.2 40.2 - - + +
157B GLN* 5.3 8.5 - - - -
158B PRO* 3.4 17.7 - - + -
159B ARG* 3.3 28.5 - - - -
160B ARG* 3.1 8.8 - - - +
161B ALA* 2.9 44.3 + - + +
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Residues in contact with ASN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 6.1 2.8 - - - +
43B TRP* 1.3 90.4 - - - +
45B ASP* 1.3 67.8 + - - +
46B LYS* 2.5 48.3 + - - +
47B GLY* 2.8 29.6 + - - +
159B ARG 3.2 17.7 - - - +
160B ARG* 4.6 9.9 - - + -
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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