Contacts of the strand formed by residues 116 - 121 (chain H) in PDB entry 1GMO
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 116 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47H LYS* 2.9 20.1 + - - -
48H THR 2.9 21.3 - - - +
49H THR* 3.5 28.9 - - + -
88H VAL* 3.7 19.3 - - + -
89H PHE 3.5 1.8 - - - -
90H ASP* 3.4 34.3 - - + -
97H LEU* 5.1 9.6 - - + -
111H GLU* 5.9 1.6 - - - -
112H PHE 4.5 2.5 - - - -
113H GLY* 2.7 25.3 + - - +
114H HIS 4.5 1.6 - - - +
115H GLU* 1.3 98.7 - - + +
117H ASP* 1.3 70.2 + - - +
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Residues in contact with ASP 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H LYS* 5.3 5.0 - - - +
45H SER 4.1 4.0 - - - -
46H ALA* 3.8 16.3 + - - +
47H LYS* 3.7 11.8 + - - +
48H THR 4.0 2.5 - - - -
88H VAL* 3.4 1.7 - - - -
89H PHE* 3.0 36.8 + - + +
114H HIS 5.4 1.0 - - - +
115H GLU 4.9 1.9 - - - +
116H PHE* 1.3 88.5 - - - +
118H LEU* 1.3 60.0 + - - +
119H TYR* 3.2 35.5 + - + +
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Residues in contact with LEU 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H LYS 3.6 0.2 - - - +
44H LYS* 3.1 6.8 - - - +
45H SER* 2.7 58.3 + - - +
48H THR* 3.7 26.2 + - + +
49H THR* 5.0 4.0 - - - +
50H LEU* 5.0 7.6 - - + +
86H ALA* 4.6 7.9 - - + -
87H PHE 4.0 4.5 - - - +
88H VAL* 3.4 25.1 - - + -
99H PHE* 5.1 2.7 - - + -
102H ASN* 6.5 0.2 - - - -
103H SER* 4.6 4.3 - - - +
110H LYS* 4.5 13.0 - - + -
117H ASP* 1.3 71.4 - - - +
119H TYR* 1.3 69.2 + - - +
120H GLU* 3.9 34.8 - - + +
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Residues in contact with TYR 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H ILE* 4.1 25.9 - - + +
42H PHE* 3.6 23.0 - - + -
43H LYS 3.8 3.1 - - - -
44H LYS* 4.5 15.9 - - + -
67H ALA* 4.0 17.2 - - + +
86H ALA* 3.2 3.2 - - - -
87H PHE* 2.9 75.6 + + + +
89H PHE* 4.3 6.8 - - + -
117H ASP* 3.2 48.8 + - + +
118H LEU* 1.3 76.7 - - - +
120H GLU* 1.3 63.4 + - - +
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Residues in contact with GLU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H PHE* 3.4 4.0 - - - -
43H LYS* 2.9 59.0 + - - +
45H SER* 4.7 4.0 + - - -
85H LYS 3.9 4.3 - - - +
86H ALA* 3.9 10.8 - - + -
102H ASN* 3.5 8.2 - - + +
103H SER* 2.4 45.7 + - - +
104H MET* 3.8 7.3 - - - +
110H LYS* 5.4 2.1 + - - -
118H LEU* 3.9 25.4 - - + +
119H TYR* 1.3 75.0 - - - +
121H ASN* 1.3 65.1 + - - +
122H LYS 3.2 1.2 + - - -
125H ILE* 3.8 15.9 - - + +
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Residues in contact with ASN 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H GLU 4.9 1.4 - - - +
42H PHE* 3.8 26.5 - - + -
74H CYS* 4.6 6.9 + - - -
75H THR* 5.4 3.4 + - - +
84H CYS 3.4 16.5 + - - +
85H LYS* 2.8 30.8 + - - +
102H ASN* 5.0 0.2 + - - -
120H GLU* 1.3 70.1 - - - +
122H LYS* 1.3 63.9 + - - +
123H ASP* 2.7 46.4 + - - +
124H TYR* 2.9 24.0 + - + +
125H ILE* 3.5 10.1 - - - +
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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