Contacts of the strand formed by residues 109 - 117 (chain G) 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 VAL 109 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22G GLU* 3.4 3.9 - - - +
23G LEU* 2.8 37.6 + - + +
47G VAL* 3.5 31.4 - - + -
48G SER 3.5 7.4 - - - +
49G LEU* 3.5 26.2 - - + -
58G HIS* 3.8 21.1 - - + -
60G VAL* 3.8 11.4 - - + -
79G LEU* 4.4 2.5 - - + -
102G LEU* 3.9 20.0 - - + -
107G GLY* 4.3 0.9 - - - -
108G PRO* 1.3 74.8 - - - +
110G HIS* 1.3 65.8 + - - +
111G ILE* 4.2 4.0 + - + -
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Residues in contact with HIS 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ILE* 5.7 2.0 - - + -
75F THR* 3.4 38.2 + - + +
103F LYS* 3.9 27.9 + - - -
21G CYS 3.6 5.3 + - - +
22G GLU* 3.8 38.5 + - + +
46G THR 3.9 0.5 - - - +
47G VAL* 3.3 4.2 - - - -
48G SER* 2.8 38.1 + - - +
49G LEU 4.5 0.7 - - - -
50G GLY* 3.6 32.0 - - - -
51G ALA 5.2 0.2 + - - -
108G PRO* 4.3 3.8 - - - +
109G VAL* 1.3 77.3 - - - +
111G ILE* 1.3 63.2 + - - +
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Residues in contact with ILE 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F VAL* 5.0 1.0 - - - +
75F THR 4.9 3.2 + - - -
19G PHE* 4.2 10.3 - - + -
20G GLY* 3.1 4.7 - - - -
21G CYS* 3.0 39.0 + - - +
23G LEU* 3.6 33.7 - - + -
44G LEU* 3.8 28.9 - - + -
46G THR 3.3 7.6 - - - +
47G VAL* 4.3 19.5 - - + -
60G VAL* 3.9 15.5 - - + -
76G LEU* 5.1 2.2 - - + -
100G LEU* 3.8 20.9 - - + -
109G VAL* 4.7 1.1 - - + -
110G HIS* 1.3 80.6 - - - +
112G SER* 1.3 64.9 + - - +
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Residues in contact with SER 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F VAL* 3.4 19.1 - - - -
75F THR 3.2 21.4 + - - -
92F PHE* 3.6 15.5 - - - -
19G PHE* 3.4 8.3 - - - -
20G GLY* 4.3 0.2 - - - -
44G LEU* 3.8 3.1 - - - -
45G ARG 2.8 21.0 + - - -
46G THR* 2.5 35.6 + - - +
111G ILE* 1.3 78.1 - - - +
113G GLY* 1.3 60.2 + - - +
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Residues in contact with GLY 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F PHE* 3.5 21.5 - - - -
18G LEU* 3.7 2.3 - - - +
19G PHE* 2.8 35.4 + - - +
43G SER 3.2 13.0 - - - -
44G LEU* 4.4 0.9 - - - -
45G ARG* 3.9 4.7 - - - -
112G SER* 1.3 77.4 - - - +
114G GLN* 1.3 64.9 + - - -
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Residues in contact with GLN 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F GLY 4.9 0.7 - - - +
92F PHE* 3.8 16.8 - - + -
93F GLU* 3.1 38.8 + - - +
16G ASN* 3.3 22.0 - - - +
17G TYR 3.4 5.2 - - - +
19G PHE* 4.2 3.4 - - - -
42G LEU* 3.6 6.4 - - - +
43G SER* 2.7 56.3 + - - +
45G ARG* 3.9 19.9 + - - +
113G GLY* 1.3 78.9 - - - -
115G HIS* 1.3 60.3 + - - +
116G LEU* 3.9 16.9 - - + +
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Residues in contact with HIS 115 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67F TYR* 3.6 34.0 - + + +
16G ASN* 3.8 0.9 - - - -
17G TYR* 2.9 45.6 + - + +
18G LEU 4.9 1.6 - - - +
19G PHE* 4.1 14.3 - + + +
31G PHE* 3.5 36.4 - + + -
34G ASP* 4.9 1.8 + - - +
40G HIS* 2.8 40.2 + + + -
41G GLN 3.6 5.7 + - - -
42G LEU* 4.8 1.3 - - - -
114G GLN* 1.3 72.5 - - - +
116G LEU* 1.3 63.8 + - - +
117G VAL* 3.9 8.5 - - + +
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Residues in contact with LEU 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G PRO* 5.1 11.9 - - + +
15G GLN 3.4 12.6 - - - +
16G ASN* 3.9 25.8 - - + +
39G GLU 3.8 0.6 - - - +
40G HIS* 3.2 6.1 - - - -
41G GLN* 2.7 49.6 + - + +
43G SER* 4.0 20.6 - - - -
93G GLU* 4.0 20.6 - - - +
114G GLN* 4.0 17.9 - - + +
115G HIS* 1.3 75.0 + - - +
117G VAL* 1.3 65.0 + - - +
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Residues in contact with VAL 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F TYR* 4.0 9.9 - - + -
14G PRO* 3.5 3.5 - - - +
15G GLN* 2.8 43.9 + - + +
17G TYR* 3.8 26.9 - - + -
38G ASN* 3.4 39.5 - - + +
39G GLU 3.4 2.7 - - - -
40G HIS* 3.6 15.7 - - + +
115G HIS* 3.9 19.7 - - + +
116G LEU* 1.3 79.4 - - - +
118G ALA* 1.3 62.3 + - - +
119G VAL 5.6 0.7 - - - -
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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