Contacts of the strand formed by residues 116 - 124 (chain C) in PDB entry 5FL6
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 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C HIS 3.2 14.6 - - - +
97C TRP* 4.2 2.5 - - + -
105C SER* 3.7 13.2 - - - +
114C PHE* 3.3 1.5 + - - +
115C PRO* 1.3 78.0 - - - +
117C GLU* 1.3 65.7 + - - +
146C PHE* 3.6 4.2 - - - -
147C LEU* 2.9 49.7 + - + +
224C LEU* 4.4 6.3 - - + -
227C LEU* 4.0 18.2 - - + -
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Residues in contact with GLU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C HIS 4.1 0.2 - - - +
95C LEU* 3.3 8.4 - - - +
96C HIS* 2.9 39.0 + - + +
105C SER* 3.6 8.4 - - - -
106C GLU* 2.8 27.1 + - - +
107C HIS* 2.8 34.0 + - - -
116C ALA* 1.3 77.4 - - - +
118C ILE* 1.3 62.9 + - - +
119C HIS* 2.6 33.1 + - + +
144C ALA* 3.7 5.3 - - - +
145C ALA 3.4 18.6 - - - +
146C PHE* 3.6 17.2 - - + -
147C LEU* 4.1 2.0 - - - +
212C VAL* 6.0 0.2 - - - -
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Residues in contact with ILE 118 (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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93C LEU* 4.2 23.1 - - + -
94C HIS 3.7 6.1 - - - +
95C LEU* 3.6 22.2 - - + -
117C GLU* 1.3 73.8 - - - +
119C HIS* 1.3 80.0 + - - +
120C VAL* 4.4 7.4 - - + -
143C LEU 3.6 0.7 - - - +
144C ALA* 3.3 2.3 - - - -
145C ALA* 2.9 56.1 + - + +
147C LEU* 4.1 4.2 - - + +
157C TYR* 3.4 31.2 - - + +
160C LEU* 5.7 0.7 - - + -
184C LEU* 4.2 21.5 - - + +
185C LEU* 4.6 7.0 - - + -
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Residues in contact with HIS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 3.1 6.1 - - - +
94C HIS* 2.9 50.4 + - + +
96C HIS* 3.2 10.3 + + - -
106C GLU* 3.2 22.2 - - + -
117C GLU* 2.6 31.5 + - + +
118C ILE* 1.3 85.7 - - - +
120C VAL* 1.3 62.3 - - - +
121C VAL* 4.0 1.0 + - - -
142C VAL* 3.7 12.3 - - + -
143C LEU 3.4 2.5 - - - -
144C ALA* 3.7 12.3 - - + -
200C THR* 4.9 0.2 - - + -
210C TRP* 3.5 22.0 - + - -
267C Y0R 3.5 2.6 + - - -
1260C ZN 2.1 32.6 - - - -
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Residues in contact with VAL 120 (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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53C PHE* 4.5 10.5 - - + -
74C LEU* 4.2 18.6 - - + -
90C ALA* 4.4 3.6 - - + -
92C GLN 3.6 8.3 - - - +
93C LEU* 4.1 15.7 - - + -
118C ILE* 4.4 8.7 - - + -
119C HIS* 1.3 74.6 - - - +
121C VAL* 1.3 60.5 + - - +
122C HIS* 3.1 31.8 + - + +
142C VAL* 3.4 2.1 - - - +
143C LEU* 2.9 40.4 + - + +
181C ILE* 5.1 3.8 - - + -
184C LEU* 6.4 0.2 - - + -
185C LEU* 4.3 25.6 - - + -
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Residues in contact with VAL 121 (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 ALA* 3.6 2.6 - - - +
91C LEU* 2.7 44.6 + - + +
92C GLN* 2.8 43.7 + - + +
94C HIS* 3.7 20.0 - - + -
120C VAL* 1.3 73.9 - - - +
122C HIS* 1.3 61.6 + - - +
140C LEU* 5.1 12.1 - - + -
141C ALA 3.9 2.5 - - - -
142C VAL* 4.2 14.8 - - + -
199C LEU* 5.9 0.2 - - + -
267C Y0R 3.7 29.4 - - - +
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Residues in contact with HIS 122 (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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53C PHE* 3.7 9.4 - + - -
80C MET* 3.5 38.9 - - + +
88C TYR* 3.7 17.3 - - + -
89C ARG 3.2 8.1 - - - +
90C ALA* 3.5 29.5 - - + +
91C LEU* 4.3 4.9 - - - +
120C VAL* 3.1 39.2 + - + -
121C VAL* 1.3 73.4 - - - +
123C LEU* 1.3 60.3 + - - +
140C LEU* 3.3 11.1 - - - +
141C ALA 2.9 37.4 + - - +
143C LEU* 3.8 21.0 - - + +
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Residues in contact with LEU 123 (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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88C TYR* 3.3 3.1 - - - -
89C ARG* 2.8 68.1 + - + +
91C LEU* 3.9 17.5 - - + +
122C HIS* 1.3 72.9 - - - +
124C SER* 1.3 79.0 + - - +
125C THR 3.4 0.2 + - - -
127C PHE* 3.6 15.7 - - + +
128C ALA 4.1 0.2 - - - +
129C ARG 3.8 9.2 - - - +
130C VAL* 3.8 25.6 - - + +
133C ALA* 3.5 31.9 - - + -
139C GLY 3.7 1.1 - - - +
140C LEU* 3.9 7.4 - - + -
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Residues in contact with SER 124 (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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87C GLU 3.6 4.1 + - - -
88C TYR* 3.2 18.4 - - - -
89C ARG* 5.5 0.2 + - - -
123C LEU* 1.3 74.7 - - - +
125C THR* 1.3 57.3 + - - +
126C ALA* 3.1 24.8 + - - +
127C PHE* 3.0 38.9 + - - +
138C GLY 3.5 15.9 - - - -
139C GLY 2.9 21.0 + - - -
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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