Contacts of the strand formed by residues 103 - 112 (chain C) in PDB entry 5UH5
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 MET 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C ILE 4.4 0.2 - - - -
97C GLU* 3.3 27.5 - - - +
98C ASP* 3.2 37.8 + - + +
101C GLY 3.9 2.9 - - - +
102C SER* 1.3 86.6 - - - +
104C SER* 1.3 62.8 + - - +
139C PHE* 3.5 22.9 - - + -
140C ILE 3.4 4.5 - - - -
141C ASN* 4.2 3.4 - - - +
404C MET* 3.6 55.2 - - + +
405C THR* 4.6 4.5 - - + +
409C VAL* 5.6 10.3 - - + -
412C ILE* 3.9 15.9 - - - -
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Residues in contact with SER 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C PRO* 3.5 16.5 - - - +
96C ILE 3.4 5.4 - - - -
97C GLU* 3.4 24.9 + - - +
101C GLY 5.4 0.2 - - - -
103C MET* 1.3 78.1 - - - +
105C LEU* 1.3 57.2 + - - +
106C SER 4.2 0.2 - - - -
139C PHE* 3.5 4.2 - - - -
140C ILE* 2.5 68.8 + - - +
142C ASN* 4.9 6.5 - - - -
404C MET* 5.3 0.2 - - - -
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C PRO* 3.3 1.1 - - - +
96C ILE* 2.5 55.3 + - + +
104C SER* 1.3 73.1 + - - +
106C SER* 1.3 63.5 + - - +
107C PHE* 3.8 25.7 - - + -
137C ALA* 4.3 6.3 - - + -
138C GLU 3.3 27.4 - - - +
139C PHE* 4.2 4.7 - - + +
400C VAL* 4.2 22.4 - - + -
404C MET* 5.5 2.2 - - - -
414C PRO* 4.1 18.2 - - + -
417C LEU* 3.9 33.7 - - + -
418C ILE* 4.3 6.5 - - + -
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C SER* 3.3 14.1 - - - -
95C PRO* 3.8 15.9 - - - -
105C LEU* 1.3 76.6 - - - +
107C PHE* 1.3 66.3 + - - +
136C THR 3.9 0.9 - - - +
137C ALA* 3.5 4.3 - - - +
138C GLU* 3.3 40.2 + - - +
140C ILE* 3.6 22.3 - - - +
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Residues in contact with PHE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LEU* 4.1 32.8 - - + +
91C TYR* 4.6 5.5 - - - -
93C LEU* 3.5 33.9 - - + -
94C SER* 2.7 25.8 + - - +
96C ILE* 4.0 15.7 - - + -
105C LEU* 3.8 26.2 - - + -
106C SER* 1.3 75.2 - - - +
108C SER* 1.3 65.8 + - - +
135C VAL* 4.4 17.0 - - + -
136C THR 3.5 3.8 - - - +
137C ALA* 3.6 19.5 - - + -
154C MET* 5.9 3.4 - - + -
393C MET* 5.3 2.2 - - + -
396C MET* 4.8 12.3 - - + -
418C ILE* 3.5 30.7 - - + -
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Residues in contact with SER 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LEU* 4.3 8.6 - - - +
91C TYR* 4.9 15.0 - - - -
107C PHE* 1.3 79.1 - - - +
109C ASP* 1.3 76.1 + - - +
110C PRO* 3.7 2.9 - - - -
135C VAL* 4.1 1.4 - - - -
136C THR* 3.1 32.9 + - - +
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Residues in contact with ASP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C TYR* 6.0 0.2 - - - -
108C SER* 1.3 82.9 - - - +
110C PRO* 1.3 72.4 - - - +
111C ARG* 2.9 51.4 + - - +
135C VAL* 3.9 2.4 - - - -
136C THR* 4.1 6.0 + - - +
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Residues in contact with PRO 110 (chain C).
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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65C ILE 5.6 1.9 - - - +
86C LEU* 4.4 20.0 - - + -
87C GLU* 4.3 26.0 - - + +
90C LEU* 4.2 16.2 - - + -
108C SER* 3.7 2.2 - - - -
109C ASP* 1.3 91.5 - - - +
111C ARG* 1.3 60.3 + - - +
112C PHE* 5.5 2.9 - - - -
133C LEU* 4.1 11.7 - - + -
134C PHE 3.3 7.9 - - - +
135C VAL* 3.8 17.0 - - + -
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Residues in contact with ARG 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ASP* 2.9 41.2 + - - +
110C PRO* 1.3 75.0 - - - +
112C PHE* 1.3 68.4 + - - +
133C LEU* 3.4 4.6 - - - +
134C PHE* 2.8 49.5 + - + +
135C VAL 4.1 1.0 - - - -
136C THR* 2.9 21.8 + - - +
151C THR* 2.6 44.0 + - - +
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Residues in contact with PHE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ILE* 3.7 43.3 - - + -
86C LEU* 3.7 28.9 - - + -
110C PRO 5.5 2.0 - - - -
111C ARG* 1.3 79.6 - - - +
113C ASP* 1.3 71.9 + - - +
131C ALA* 3.4 24.0 - - + +
132C PRO 3.5 6.5 - - - +
133C LEU* 3.7 25.6 - - + -
134C PHE* 5.4 2.5 - - - -
157C PHE* 3.7 22.9 - + - -
159C MET* 4.9 9.4 - - + -
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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