Contacts of the strand formed by residues 96 - 101 (chain B) in PDB entry 5FQD
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 THR 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B THR 5.8 0.7 - - - +
57B HIS* 4.3 23.1 - - + +
91B LEU* 5.0 0.2 - - - +
94B GLY 3.9 4.3 + - - -
95B GLN* 1.3 80.3 - - - +
97B LEU* 1.3 66.9 - - - +
98B PRO* 3.9 2.2 - - - +
142B TYR* 3.0 32.3 + - + +
158B LYS* 4.8 3.4 - - + -
159B ALA 3.4 9.0 - - - +
160B ILE* 4.6 5.9 - - - +
343B CYS* 6.0 2.8 - - - -
348B ALA* 3.9 22.3 + - - +
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Residues in contact with LEU 97 (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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87B VAL* 4.4 11.7 - - + -
89B MET* 3.7 30.1 - - + -
91B LEU* 4.0 17.5 - - + -
95B GLN 3.7 0.6 + - - -
96B THR* 1.3 75.4 - - - +
98B PRO* 1.4 72.9 - - + +
99B LEU* 3.8 22.9 - - + +
120B PHE* 4.5 11.4 - - + -
122B VAL* 4.3 23.6 - - + -
157B VAL 3.8 0.9 - - - +
158B LYS* 3.7 1.1 - - - -
159B ALA* 2.8 42.8 + - + +
348B ALA* 4.7 0.4 - - + -
356B VAL* 3.9 21.5 - - + -
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Residues in contact with PRO 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B HIS* 3.6 23.8 - - + +
59B TYR* 3.9 8.5 - - - +
60B LEU* 4.3 10.8 - - + -
96B THR* 3.9 4.0 - - - +
97B LEU* 1.4 90.5 - - + +
99B LEU* 1.3 71.1 + - - +
157B VAL 3.4 8.3 - - - +
158B LYS* 4.4 4.9 - - + -
348B ALA* 3.6 31.0 - - + +
349B TYR* 3.9 7.0 - - - +
350B VAL* 3.7 17.1 - - + +
356B VAL* 3.5 12.2 - - + +
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Residues in contact with LEU 99 (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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60B LEU* 5.2 1.2 - - - +
84B LEU* 3.5 31.9 - - + -
87B VAL* 4.1 17.9 - - + -
97B LEU* 3.8 24.9 - - + +
98B PRO* 1.3 88.2 - - - +
100B GLN* 1.3 65.4 + - - +
101B LEU* 4.0 15.5 - - + -
120B PHE* 3.9 19.7 - - + -
155B VAL 4.6 0.4 - - - -
156B LYS* 3.3 4.5 - - - +
157B VAL* 2.8 49.4 + - + +
350B VAL* 4.1 5.5 - - - +
354B GLY 5.6 2.0 - - - +
356B VAL* 4.0 11.2 - - + -
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Residues in contact with GLN 100 (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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60B LEU* 3.6 27.9 - - + +
99B LEU* 1.3 75.8 - - - +
101B LEU* 1.3 65.8 + - - +
102B PHE* 3.4 41.7 - - + -
106B GLU* 5.3 0.2 - - - +
154B ILE* 4.5 4.2 - - + +
155B VAL 3.7 4.0 - - - -
156B LYS* 3.5 29.8 - - + +
350B VAL* 3.8 11.6 - - + +
351B ASN 3.7 11.9 + - - -
352B PRO* 4.2 5.9 - - - +
354B GLY* 3.7 17.4 + - - +
378B HIS* 3.6 22.2 + - - -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.8 28.0 - - + -
87B VAL* 5.8 2.2 - - + -
99B LEU* 4.0 25.1 - - + -
100B GLN* 1.3 78.8 - - - +
102B PHE* 1.3 60.0 + - - +
106B GLU* 3.9 31.2 - - + +
107B VAL* 3.8 5.4 - - + +
110B VAL* 3.4 33.4 - - + -
154B ILE* 3.6 8.7 - - - +
155B VAL* 2.8 52.5 + - + +
157B VAL* 5.2 3.6 - - + -
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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