Contacts of the strand formed by residues 128 - 137 (chain H) in PDB entry 3F5O
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 LEU 128 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E LEU* 3.7 39.9 - - + +
108E LYS* 5.4 3.4 - - + +
91H MET* 3.4 43.3 - - + +
92H SER* 2.9 21.6 + - - -
119H ASP* 4.0 22.9 - - - +
120H LEU 3.7 7.9 - - - +
121H THR* 4.0 13.5 - - + -
126H GLY 3.6 2.0 + - - -
127H LYS* 1.3 73.4 - - - +
129H ILE* 1.4 60.0 + - - +
130H ALA 3.6 18.6 - - - +
131H GLN* 4.8 3.8 - - + +
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Residues in contact with ILE 129 (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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55H LEU* 4.8 10.5 - - + -
60H THR* 5.3 2.9 - - + +
90H TYR* 3.8 4.1 - - + +
91H MET* 2.9 24.3 + - - -
92H SER* 3.3 30.7 + - - +
93H PRO 4.6 3.6 - - - +
94H ALA* 3.7 23.6 - - + +
98H GLU* 5.2 2.2 - - - +
100H ILE* 3.4 33.4 - - + -
120H LEU* 2.7 20.5 + - + +
121H THR* 3.7 19.7 - - - +
122H ASN* 3.7 13.5 - - + +
127H LYS 3.3 1.1 + - - +
128H LEU* 1.4 73.9 - - - +
130H ALA* 1.3 66.3 + - + +
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Residues in contact with ALA 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H THR* 3.8 28.9 - - + -
88H ILE* 4.1 7.2 - - + -
89H THR 3.1 16.8 - - - +
90H TYR* 4.3 5.8 - - + -
91H MET* 3.8 6.5 - - - -
120H LEU* 2.9 35.5 + - + +
128H LEU* 3.6 7.2 - - - +
129H ILE* 1.3 85.2 - - + +
131H GLN* 1.3 61.7 + - - +
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Residues in contact with GLN 131 (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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107E LEU* 3.7 24.6 - - - +
117E SER* 4.0 13.6 + - - -
131E GLN* 5.4 7.5 - - - +
133E ARG* 2.8 43.3 - - - +
64H VAL* 5.3 0.7 - - - -
88H ILE* 3.4 4.8 - - - -
89H THR 2.8 31.6 + - - -
91H MET* 3.6 12.7 - - + +
117H SER* 5.8 3.6 - - - -
118H VAL 3.3 5.4 - - - +
119H ASP* 3.0 29.3 - - - +
128H LEU* 4.8 4.1 - - + +
130H ALA* 1.3 76.7 - - - +
132H GLY* 1.3 65.3 + - - +
133H ARG* 5.5 0.4 - - - +
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Residues in contact with GLY 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ARG* 3.4 7.6 + - - -
64H VAL* 4.3 19.7 - - - +
87H ASN 3.0 14.8 - - - -
88H ILE* 4.1 2.0 - - - -
117H SER* 3.4 5.4 - - - -
118H VAL 2.8 33.4 + - - +
131H GLN* 1.3 76.4 - - - +
133H ARG* 1.3 60.4 + - - +
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Residues in contact with ARG 133 (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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87E ASN* 2.8 30.2 + - - -
88E ILE 4.3 0.6 - - - -
89E THR* 2.8 41.6 + - + +
117E SER* 5.5 0.6 + - - -
131E GLN* 2.8 43.3 + - - +
132E GLY* 3.4 9.5 + - - +
133E ARG* 3.3 34.3 - - - +
64H VAL* 4.7 0.2 - - - +
85H ASP 4.6 0.2 - - - -
86H MET* 3.3 5.6 - - - +
87H ASN* 3.0 49.2 + - - +
107H LEU* 4.2 9.6 - - + -
115H PHE* 6.0 0.7 - - + -
116H THR 3.2 21.5 - - - +
117H SER* 4.5 0.7 - - - -
118H VAL* 6.3 0.2 - - - -
131H GLN* 5.5 0.6 - - - +
132H GLY* 1.3 74.6 - - - +
134H HIS* 1.3 64.2 + - - +
135H THR* 5.7 0.7 - - - +
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Residues in contact with HIS 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H VAL* 4.6 5.8 - - + -
65H ASP* 3.2 33.2 + - - -
68H SER* 2.9 23.1 + - - +
83H SER* 2.7 27.9 + - - -
85H ASP 3.4 13.9 - - - -
86H MET* 4.0 18.6 - - + +
114H ALA 4.0 0.7 - - - +
115H PHE* 3.8 0.9 - - - -
116H THR* 2.9 46.5 + - + +
133H ARG* 1.3 77.9 - - - +
135H THR* 1.3 66.6 + - - +
136H LYS* 3.5 28.7 + - + +
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Residues in contact with THR 135 (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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89E THR* 3.9 3.3 + - - +
84F VAL* 4.0 9.0 - - + -
85F ASP* 2.7 34.1 + - - +
84H VAL* 2.9 30.2 + - + -
85H ASP 2.8 17.2 + - - +
113H LEU* 4.2 15.9 - - + -
114H ALA 3.4 7.9 - - - +
115H PHE* 3.5 31.6 - - + +
133H ARG* 4.3 0.9 - - - +
134H HIS* 1.3 74.5 + - - +
136H LYS* 1.3 63.4 + - - +
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Residues in contact with LYS 136 (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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65H ASP* 4.7 0.4 + - - -
68H SER* 5.3 0.2 - - - +
69H THR* 2.8 26.7 + - - +
72H LEU* 3.6 25.1 - - + -
80H PRO 2.8 27.8 + - - +
81H GLY* 3.2 9.8 + - - -
82H VAL 3.2 16.2 - - - +
83H SER 3.7 0.4 - - - +
84H VAL* 4.1 3.4 - - - +
113H LEU* 3.3 7.1 - - - +
114H ALA* 2.9 33.4 + - + +
116H THR* 5.5 0.2 - - + -
134H HIS* 3.5 35.6 - - + +
135H THR* 1.3 78.2 - - - +
137H HIS* 1.3 60.7 + - - +
138H LEU* 3.9 2.8 + - + -
149H UOC 2.8 28.6 + - - -
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Residues in contact with HIS 137 (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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112F THR* 3.7 25.0 + - + -
113F LEU* 4.3 7.0 - - + +
81H GLY* 3.2 2.6 - - - -
82H VAL* 2.8 37.8 + - + +
84H VAL* 3.5 21.2 - - + +
112H THR* 3.3 20.9 + - + -
113H LEU* 4.0 4.9 - - + +
136H LYS* 1.3 72.5 - - - +
138H LEU* 1.3 61.3 + - - +
139H GLY* 3.4 25.9 - - - -
150H COA 3.3 61.2 + - + -
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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