Contacts of the strand formed by residues 130 - 141 (chain C) in PDB entry 5UH8
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 ALA 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C VAL* 3.3 8.9 - - - +
116C LYS* 3.2 33.2 + - + +
117C ALA 5.9 0.2 - - - +
122C CYS* 5.2 0.2 - - - -
128C THR* 3.1 17.9 + - + +
129C TYR* 1.3 78.3 - - - +
131C ALA* 1.3 60.4 + - - +
132C PRO* 4.6 0.2 - - - -
156C ASP* 4.1 13.9 - - + +
157C PHE 3.2 30.1 - - - +
158C PRO* 3.7 2.9 - - + -
159C MET* 4.0 3.6 - - - +
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Residues in contact with ALA 131 (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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112C PHE* 3.9 13.2 - - + -
113C ASP 3.6 21.5 - - - +
115C VAL* 4.1 14.1 - - + +
130C ALA* 1.3 75.1 - - - +
132C PRO* 1.3 68.3 - - + +
156C ASP* 4.5 0.4 - - - -
157C PHE* 2.9 32.4 + - - +
159C MET* 3.8 20.0 - - + +
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Residues in contact with PRO 132 (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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112C PHE* 3.6 3.3 - - - -
113C ASP* 3.1 46.6 + - + +
114C ASP 3.4 16.8 - - - +
116C LYS* 3.8 20.0 - - + -
131C ALA* 1.3 83.5 - - + +
133C LEU* 1.3 62.6 + - - +
134C PHE* 4.9 6.2 - - + -
153C PHE* 3.6 13.9 - - + -
155C GLY 3.6 6.7 - - - +
156C ASP* 3.6 17.2 - - - +
391F GLY 4.1 9.4 - - - +
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Residues in contact with LEU 133 (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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86C LEU* 4.3 15.7 - - + -
110C PRO* 4.3 10.3 - - + -
111C ARG 3.7 15.9 - - - +
112C PHE* 3.8 28.9 - - + -
131C ALA 3.5 0.8 + - - -
132C PRO* 1.3 71.9 - - - +
134C PHE* 1.3 84.6 + - - +
135C VAL* 4.9 3.6 - - + -
153C PHE* 3.3 1.7 - - - -
154C MET* 3.1 47.9 + - + +
155C GLY 3.0 14.3 + - - +
157C PHE* 4.3 24.0 - - + -
423C VAL* 6.5 0.2 - - + -
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Residues in contact with PHE 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C PRO* 3.2 0.5 - - - +
111C ARG* 2.7 63.4 + - + +
112C PHE 5.4 0.4 - - - -
113C ASP* 3.4 37.2 - - + -
132C PRO* 4.9 7.4 - - + -
133C LEU* 1.3 83.2 - - - +
135C VAL* 1.3 70.3 + - - +
151C THR* 4.2 17.3 - - + -
152C VAL 3.8 4.5 - - - -
153C PHE* 3.3 39.7 - + + -
391F GLY* 4.5 16.4 - - - -
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Residues in contact with VAL 135 (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* 4.2 19.5 - - + -
107C PHE* 4.7 17.5 - - + -
108C SER 4.3 3.4 - - - +
109C ASP 3.8 6.1 - - - -
110C PRO* 3.8 20.4 - - + -
111C ARG* 4.2 2.9 - - - -
133C LEU* 4.9 5.4 - - + -
134C PHE* 1.3 79.0 - - - +
136C THR* 1.3 60.3 + - - +
151C THR* 3.2 5.4 - - - +
152C VAL* 2.8 47.1 + - + +
154C MET* 3.6 28.9 - - + -
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Residues in contact with THR 136 (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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106C SER 3.9 0.9 - - - +
107C PHE* 3.5 3.3 - - - +
108C SER* 3.0 46.6 + - - +
109C ASP* 3.8 5.5 + - - +
111C ARG* 2.9 29.1 + - - -
135C VAL* 1.3 72.1 - - - +
137C ALA* 1.3 61.9 + - - +
138C GLU* 5.9 0.3 - - - +
149C SER* 3.9 18.4 - - - +
150C GLN* 3.6 13.9 - - - +
151C THR* 4.2 2.2 - - - +
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Residues in contact with ALA 137 (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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105C LEU* 4.3 2.5 - - + -
106C SER 3.6 5.2 - - - +
107C PHE* 3.6 29.8 - - + -
135C VAL* 4.0 1.3 + - + +
136C THR* 1.3 75.6 - - - +
138C GLU* 1.3 57.2 + - - +
149C SER* 3.5 2.0 - - - -
150C GLN 2.7 41.3 + - - +
152C VAL* 3.8 22.4 - - + -
414C PRO* 3.6 18.6 - - + +
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Residues in contact with GLU 138 (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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104C SER 3.6 0.5 - - - +
105C LEU* 3.3 16.5 - - - +
106C SER* 3.3 35.2 + - - +
136C THR* 6.1 0.2 - - + -
137C ALA* 1.3 75.0 - - - +
139C PHE* 1.3 60.5 + - - +
140C ILE* 3.6 18.8 + - + +
147C ILE* 4.0 22.1 - - + +
148C LYS 3.3 4.5 - - - +
149C SER* 3.5 26.8 + - - +
414C PRO* 4.8 0.4 - - - -
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Residues in contact with PHE 139 (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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103C MET* 3.7 40.4 - - + -
104C SER 3.7 11.0 - - - -
105C LEU* 4.3 5.2 - - + -
138C GLU* 1.3 70.8 - - - +
140C ILE* 1.3 64.0 + - - +
141C ASN* 3.7 18.2 + - + -
146C GLU* 3.8 3.7 - - + +
147C ILE* 3.7 6.0 - - - -
148C LYS* 2.9 37.2 + - + +
404C MET* 4.8 1.8 - - - -
409C VAL* 4.0 13.7 - - + -
412C ILE* 3.5 53.6 - - + +
414C PRO* 4.1 17.0 - - + +
417C LEU* 3.8 15.0 - - + -
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Residues in contact with ILE 140 (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* 5.9 0.9 - - + -
103C MET* 3.4 1.4 - - - -
104C SER* 2.5 64.2 + - - +
106C SER* 4.0 12.1 - - - +
138C GLU* 3.7 29.8 - - + +
139C PHE* 1.3 75.2 - - - +
141C ASN* 1.3 64.6 + - - +
142C ASN* 4.2 16.2 - - - +
145C GLY 6.4 0.2 - - - -
147C ILE* 4.1 27.6 - - + -
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Residues in contact with ASN 141 (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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102C SER* 2.3 48.9 + - - -
103C MET* 3.9 7.3 - - - +
139C PHE* 4.2 15.0 - - + -
140C ILE* 1.3 79.3 - - - +
142C ASN* 1.3 61.9 + - - +
143C ASN* 3.6 4.1 - - - +
144C THR* 2.5 45.9 + - - +
145C GLY* 2.9 29.5 + - - -
146C GLU* 3.5 12.1 + - + +
409C VAL* 3.5 15.1 - - + +
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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