Contacts of the strand formed by residues 15 - 23 (chain B) in PDB entry 5EHD
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 GLN 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PRO* 1.3 81.2 - - - +
16B ASN* 1.3 61.2 + - - +
17B TYR* 3.6 31.6 - - + +
116B LEU* 3.3 5.9 - - - +
117B VAL* 2.9 42.5 + - + +
118B ALA 5.2 5.4 - - - -
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Residues in contact with ASN 16 (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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41A GLN* 3.1 27.2 + - - +
93A GLU* 3.1 30.5 - - - +
94A ILE* 4.1 2.1 + - - -
95A THR* 3.2 24.2 + - - -
14B PRO 4.7 5.5 + - - +
15B GLN* 1.3 76.5 - - - +
17B TYR* 1.3 69.7 + - - +
114B GLN* 3.6 12.4 - - + +
115B HIS 3.3 4.3 - - - +
116B LEU* 3.5 22.9 - - + -
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Residues in contact with TYR 17 (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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65A MET* 3.9 8.7 - - + +
66A ASN* 3.7 9.4 - - - -
67A TYR* 3.6 65.1 - + + +
95A THR* 6.2 0.7 - - - +
15B GLN* 3.6 37.4 - - + +
16B ASN* 1.3 81.5 - - - +
18B LEU* 1.3 61.3 + - - +
114B GLN* 3.3 6.7 - - - +
115B HIS* 2.7 43.2 + - + +
117B VAL* 3.9 9.3 - - + +
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Residues in contact with LEU 18 (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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62A ALA* 4.2 27.6 - - + +
64A ALA* 3.7 30.3 - - + +
65A MET 3.4 14.8 + - - +
66A ASN* 3.6 23.7 - - - +
67A TYR 4.7 0.2 + - - -
72A ILE* 4.1 9.5 - - + +
74A VAL* 4.2 15.7 - - + -
92A PHE* 3.6 36.8 - - + -
93A GLU 5.4 0.7 - - - +
94A ILE* 3.9 26.2 - - + +
17B TYR* 1.3 76.3 - - - +
19B PHE* 1.3 63.7 + - - +
113B GLY 3.7 6.5 - - - +
114B GLN* 4.8 0.4 - - - +
115B HIS* 4.8 2.4 - - - +
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Residues in contact with PHE 19 (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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72A ILE* 4.5 4.3 - - + -
74A VAL* 3.4 14.0 - - - +
18B LEU* 1.3 74.5 - - - +
20B GLY* 1.3 72.8 + - - +
21B CYS* 3.9 19.5 - - - -
29B TYR* 3.4 44.4 - + - -
31B PHE* 4.2 12.8 - + - -
42B LEU* 3.4 30.7 - - + -
44B LEU* 4.2 15.5 - - + -
100B LEU* 4.4 5.8 - - + -
111B ILE* 4.3 5.6 - - + -
112B SER* 3.6 1.0 - - - -
113B GLY* 2.8 48.0 + - - +
114B GLN 4.1 1.3 - - - -
115B HIS* 4.1 16.6 - - + +
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Residues in contact with GLY 20 (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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72A ILE* 3.5 21.3 - - - +
73A LYS 5.4 2.0 - - - -
74A VAL* 3.5 16.2 - - - -
19B PHE* 1.3 89.3 - - - +
21B CYS* 1.3 66.6 + - - +
29B TYR* 4.9 2.9 + - - -
111B ILE 3.1 13.0 - - - -
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Residues in contact with CYS 21 (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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19B PHE* 3.9 18.8 - - + -
20B GLY* 1.3 76.0 - - - +
22B GLU* 1.3 60.7 + - - +
23B LEU* 4.3 5.8 - - - -
29B TYR* 3.8 44.2 - - + -
100B LEU* 4.2 5.2 - - - -
109B VAL 3.9 0.3 - - - +
110B HIS* 3.3 7.4 - - - +
111B ILE* 2.8 51.9 + - - +
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Residues in contact with GLU 22 (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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103A LYS* 4.9 2.6 + - - -
21B CYS* 1.3 77.3 - - - +
23B LEU* 1.3 68.9 + - - +
24B LYS* 3.4 28.8 + - + +
27B LYS* 3.1 34.1 + - - +
29B TYR* 5.3 2.8 - - - +
108B PRO* 3.7 27.3 - - + +
109B VAL 3.3 4.3 - - - +
110B HIS* 3.2 29.2 + - + -
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Residues in contact with LEU 23 (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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21B CYS* 4.3 4.0 - - - -
22B GLU* 1.3 76.7 - - - +
24B LYS* 1.3 68.3 + - - +
27B LYS 3.9 11.7 - - - +
29B TYR* 3.6 22.9 - - + -
60B VAL* 4.0 22.0 - - + -
100B LEU* 3.4 29.2 - - + +
101B ARG* 3.7 27.4 - - - +
102B LEU* 3.9 20.7 - - + +
108B PRO* 3.5 0.9 - - - +
109B VAL* 2.7 40.0 + - + +
111B ILE* 4.2 13.7 - - + -
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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
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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