Contacts of the strand formed by residues 95 - 99 (chain F) 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 GLN 95 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61F THR* 4.0 23.2 + - - +
62F LYS 3.6 7.8 + - - +
63F LYS* 3.5 18.3 + - + +
64F VAL* 3.8 1.6 - - - +
89F PHE* 3.8 8.6 - - - -
90F ASP* 3.1 38.1 + - + -
93F ARG* 4.1 33.8 - - + +
94F LYS* 1.3 78.4 - - - +
96F CYS* 1.3 58.7 + - - +
97F LEU* 3.4 24.0 - - + +
3M SGN 5.7 0.3 + - - -
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Residues in contact with CYS 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F THR* 3.1 25.5 - - - -
62F LYS 3.1 9.4 + - - +
64F VAL* 3.9 22.4 - - - -
70F CYS* 2.0 59.9 - - + -
87F PHE* 5.4 0.2 - - + -
88F VAL 3.8 1.8 - - - -
95F GLN* 1.3 69.4 - - - +
97F LEU* 1.3 69.6 + - - +
98F TRP* 3.4 32.8 - - + +
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Residues in contact with LEU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F THR* 5.0 5.8 - - - +
50F LEU 6.0 0.7 - - - +
59F ILE* 4.7 2.5 - - + -
60F LYS 4.0 2.7 - - - -
61F THR* 3.8 17.0 - - + -
87F PHE* 3.2 5.3 - - - +
88F VAL* 3.0 45.3 + - + +
90F ASP* 4.6 8.1 - - + -
95F GLN* 3.4 32.5 - - + +
96F CYS* 1.3 84.2 - - - +
98F TRP* 1.3 63.1 + - - +
99F PHE* 3.4 31.8 - - + -
116F PHE* 5.0 8.7 - - + -
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Residues in contact with TRP 98 (chain F).
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* 3.8 1.6 - - - -
60F LYS* 2.9 52.3 + - + +
61F THR* 4.1 3.6 - - - -
62F LYS* 3.6 29.4 - - + -
69F GLN 4.4 1.1 - - - -
70F CYS* 2.9 25.9 + - - +
73F ARG* 3.5 48.2 - - + -
74F CYS* 3.8 18.2 - - + +
80F LEU* 3.9 25.8 - - + -
82F PHE* 3.6 7.8 - - + -
84F CYS* 3.9 7.6 - - - -
86F ALA 3.8 2.7 - - - -
87F PHE* 3.6 18.8 - - + -
96F CYS* 3.4 31.2 - - + -
97F LEU* 1.3 71.1 - - - +
99F PHE* 1.3 64.2 + - - +
4M IDS 5.0 0.4 - - - -
6M IDS 4.2 6.3 - - - -
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Residues in contact with PHE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F THR* 4.9 0.2 - - - -
50F LEU* 3.3 42.4 - - + -
59F ILE* 3.4 35.0 - - + -
82F PHE* 3.9 2.9 - - - -
84F CYS* 3.4 6.8 - - - -
85F LYS 3.0 21.7 + - - -
86F ALA* 2.8 24.9 + - + +
87F PHE 4.5 0.4 - - - -
88F VAL* 3.2 35.4 - - + -
97F LEU* 3.4 31.6 - - + -
98F TRP* 1.3 73.3 - - - +
100F PRO* 1.3 63.9 - - - +
101F PHE* 3.2 37.0 + + + +
118F LEU* 5.0 0.4 - - + -
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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