Contacts of the strand formed by residues 99 - 104 (chain E) in PDB entry 5GLF
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 99 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E ARG* 3.7 49.4 - - + +
26E LEU 3.3 8.7 - - - +
27E ILE* 3.7 23.1 - - + -
60E LYS 4.8 0.5 - - - +
61E GLY* 5.1 3.3 - - - -
62E LYS* 5.5 3.7 - - - +
94E VAL* 4.5 6.1 - - - +
97E GLY 4.6 1.8 - - - +
98E ASP* 1.3 79.9 - - - +
100E ILE* 1.3 79.2 + - - +
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Residues in contact with ILE 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ARG* 3.2 8.2 - - - +
26E LEU* 2.9 44.3 + - + +
28E VAL* 3.8 16.4 - - + -
59E LEU* 4.4 7.0 - - + -
60E LYS 3.3 17.3 - - - +
61E GLY* 4.1 4.0 - - - -
82E ILE* 3.9 37.2 - - + -
84E MET* 4.0 8.5 - - + -
92E LEU* 4.5 9.9 - - + -
94E VAL* 3.9 21.1 - - + -
99E VAL* 1.3 81.1 - - - +
101E SER* 1.3 76.6 + - - +
102E ILE* 4.3 4.0 - - + +
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Residues in contact with SER 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ASN 3.2 14.4 - - - -
25E ARG* 4.1 12.3 - - - -
58E LEU 3.8 0.6 - - - +
59E LEU* 3.3 5.0 - - - -
60E LYS* 2.9 57.6 + - - +
100E ILE* 1.3 80.6 - - - +
102E ILE* 1.3 62.4 + - - +
103E GLN* 4.9 3.3 + - - -
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Residues in contact with ILE 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E ASN* 2.9 35.0 + - + +
26E LEU* 3.8 17.5 - - + -
39E VAL* 4.9 1.6 - - + -
41E LEU* 4.0 24.0 - - + -
49E LEU* 3.8 23.4 - - + +
51E LEU* 4.4 4.9 - - + -
57E VAL* 3.9 29.2 - - + -
58E LEU 3.5 3.4 - - - -
59E LEU* 3.7 25.1 - - + -
71E VAL* 5.1 0.2 - - + -
82E ILE* 4.3 10.1 - - + -
100E ILE* 4.4 3.1 - - + -
101E SER* 1.3 76.4 - - - +
103E GLN* 1.3 70.1 + - - +
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Residues in contact with GLN 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E LEU* 6.2 1.1 - - - -
51E LEU* 5.1 1.1 - - - -
57E VAL* 3.4 5.9 - - - +
58E LEU* 2.8 56.6 + - + +
60E LYS* 3.2 34.2 + - - +
101E SER* 4.9 2.4 + - - -
102E ILE* 1.3 82.6 - - - +
104E PRO* 1.3 83.1 + - + +
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Residues in contact with PRO 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E LEU* 4.7 12.1 - - + +
50E GLN* 5.7 2.5 - - + +
51E LEU* 4.0 26.2 - - + -
55E ASP* 5.9 1.3 - - + +
56E THR 4.0 5.8 - - - +
58E LEU* 4.8 0.3 - - - +
103E GLN* 1.3 104.1 + - + +
105E CYS* 1.3 60.8 + - - +
106E PRO* 3.6 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