Contacts of the strand formed by residues 116 - 124 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 5.9 0.2 - - + -
96B HIS 3.2 15.5 - - - +
97B TRP* 4.0 2.7 - - + -
105B SER* 3.8 11.0 - - - +
114B PHE* 3.2 3.3 + - - +
115B PRO* 1.3 82.0 - - - +
117B GLU* 1.3 63.5 + - - +
146B PHE* 3.6 3.5 - - - -
147B LEU* 2.9 48.4 + - + +
224B LEU* 4.4 6.7 - - + -
227B LEU* 4.0 17.7 - - + -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.3 8.0 - - - +
96B HIS* 2.9 37.5 + - + +
105B SER* 3.5 13.8 - - - -
106B GLU* 2.8 28.2 + - - +
107B HIS* 2.8 34.9 + - - -
116B ALA* 1.3 77.0 - - - +
118B ILE* 1.3 63.3 + - - +
119B HIS* 2.7 35.2 + - + +
144B ALA* 3.7 5.3 - - - +
145B ALA 3.3 18.6 - - - +
146B PHE* 3.5 11.2 - - + -
147B LEU* 4.1 2.2 - - - +
212B VAL* 6.0 0.4 - - - -
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 4.1 24.9 - - + -
94B HIS 3.6 10.3 - - - +
95B LEU* 3.5 17.0 - - + -
117B GLU* 1.3 74.2 - - - +
119B HIS* 1.3 73.2 + - - +
120B VAL* 4.5 8.3 - - + -
143B LEU 3.6 0.9 - - - +
144B ALA* 3.2 7.3 - - - -
145B ALA* 2.9 55.5 + - + +
147B LEU* 4.0 3.7 - - + +
157B TYR* 3.4 30.3 - - + +
184B LEU* 4.1 22.0 - - + +
185B LEU* 4.5 7.4 - - + -
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.1 5.0 - - - +
94B HIS* 2.9 48.8 + - + +
96B HIS* 3.2 10.2 + + - -
106B GLU* 3.1 22.4 - - + -
107B HIS* 5.2 0.2 - - - -
117B GLU* 2.7 32.8 + - + +
118B ILE* 1.3 85.0 - - - +
120B VAL* 1.3 62.7 - - - +
121B VAL 3.9 0.8 + - - -
142B VAL* 3.7 13.5 - - + -
143B LEU 3.4 2.0 - - - -
144B ALA* 3.7 12.1 - - + -
210B TRP* 3.6 19.9 - + - -
269B Y0R 3.4 2.6 + - - -
1260B ZN 2.1 33.1 - - - -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 4.6 9.9 - - + -
74B LEU* 4.2 17.9 - - + -
90B ALA* 4.4 4.0 - - + -
92B GLN 3.6 9.0 - - - +
93B LEU* 4.1 16.6 - - + -
118B ILE* 4.5 8.7 - - + -
119B HIS* 1.3 74.1 - - - +
121B VAL* 1.3 60.5 + - - +
122B HIS* 3.0 31.4 + - + +
142B VAL* 3.3 2.5 - - - -
143B LEU* 2.9 43.6 + - + +
181B ILE* 5.0 3.6 - - + -
185B LEU* 4.3 26.2 - - + -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ALA* 3.7 2.4 - - - -
91B LEU* 2.8 36.0 + - + +
92B GLN* 2.9 30.6 + - + +
94B HIS* 3.6 31.2 - - + -
119B HIS 4.5 0.7 - - - +
120B VAL* 1.3 73.6 - - - +
122B HIS* 1.3 68.7 + - - +
140B LEU* 5.1 11.9 - - + -
141B ALA 3.9 2.2 - - - -
142B VAL* 4.3 14.6 - - + -
199B LEU* 5.8 0.2 - - + -
269B Y0R 3.7 33.7 - - - +
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Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PHE* 3.9 8.8 - + - -
80B MET* 3.6 39.9 - - + +
88B TYR* 3.7 17.5 - - + -
89B ARG 3.3 7.2 - - - +
90B ALA* 3.5 29.1 - - + +
91B LEU* 4.4 3.1 - - - +
120B VAL* 3.0 46.3 + - + -
121B VAL* 1.3 75.5 - - - +
123B LEU* 1.3 60.1 + - - +
140B LEU* 3.3 14.0 - - - +
141B ALA 2.8 39.4 + - - +
143B LEU* 3.7 21.7 - - + +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B TYR* 3.3 3.8 - - - -
89B ARG* 2.9 67.6 + - + +
91B LEU* 4.0 18.3 - - + +
122B HIS* 1.3 71.8 - - - +
124B SER* 1.3 75.8 + - - +
127B PHE* 3.7 15.7 - - + +
128B ALA 3.9 6.7 - - - +
129B ARG 3.9 15.5 - - - +
130B VAL* 4.0 12.8 - - + +
133B ALA* 3.5 31.6 - - + -
139B GLY 3.8 0.7 - - - -
140B LEU* 3.7 10.3 - - + -
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PRO* 3.9 9.2 - - - +
87B GLU 3.6 3.6 + - - -
88B TYR* 3.3 17.4 - - - -
89B ARG* 5.8 0.6 + - - -
123B LEU* 1.3 75.6 - - - +
125B THR* 1.3 58.7 + - - +
126B ALA* 3.0 22.7 + - - +
127B PHE* 3.1 39.0 + - - +
138B GLY 3.6 16.6 - - - -
139B GLY 2.8 21.8 + - - -
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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