Contacts of the strand formed by residues 114 - 120 (chain L) in PDB entry 6AHU
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 LYS 114 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109L LEU* 4.3 2.0 - - - -
110L LEU* 3.3 51.6 + - + +
112L ASN* 4.5 18.8 - - + +
113L GLY* 1.3 75.8 - - - +
115L LEU* 1.3 61.5 + - - +
116L ILE* 3.0 19.1 + - + -
147L SER* 4.5 11.2 - - - +
148L ILE 3.3 5.4 - - - +
149L ASP* 3.7 30.3 - - + +
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Residues in contact with LEU 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74L LEU* 5.6 4.5 - - + +
77L LEU* 5.3 14.8 - - + -
78L ILE* 4.1 26.7 - - + -
94L ALA* 5.9 0.2 - - + -
107L VAL* 3.8 23.6 - - + -
108L ALA 3.4 18.6 - - - +
109L LEU* 3.8 23.5 - - + +
113L GLY 3.7 2.4 + - - -
114L LYS* 1.3 67.7 - - - +
116L ILE* 1.3 58.4 + - - +
117L LEU* 3.7 7.9 + - + +
146L VAL 3.6 3.6 - - - +
148L ILE* 2.5 53.9 + - + +
150L LEU* 4.2 12.1 - - + -
169L PHE* 4.8 9.0 - - + -
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Residues in contact with ILE 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ALA* 2.9 34.5 + - - +
110L LEU* 3.7 35.4 - - + -
114L LYS* 3.0 18.0 + - + +
115L LEU* 1.3 71.2 - - - +
117L LEU* 1.3 60.0 + - - +
145L ILE* 3.7 25.8 - - + -
146L VAL 3.4 3.8 - - - +
147L SER* 3.4 28.7 - - - +
321L PRO* 5.1 3.9 - - + +
322L VAL* 3.8 30.1 - - + -
325L GLU 5.8 2.0 - - - +
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Residues in contact with LEU 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74L LEU* 4.5 11.9 - - + -
106L THR 3.5 4.0 - - - -
107L VAL* 3.7 35.4 - - + +
115L LEU* 4.0 14.1 - - + +
116L ILE* 1.3 74.3 - - - +
118L SER* 1.3 60.1 + - - +
119L LEU* 3.8 36.5 + - + +
129L LEU* 4.9 2.2 - - + -
145L ILE* 3.4 5.8 - - - +
146L VAL* 3.0 60.6 + - + +
148L ILE* 4.1 17.0 - - + -
169L PHE* 4.7 10.3 - - + -
175L LEU* 5.7 0.2 - - + -
321L PRO* 6.0 0.4 - - - -
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Residues in contact with SER 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L ILE* 4.0 24.8 + - - +
105L ASN* 3.6 2.3 - - - -
106L THR* 2.6 43.2 + - - +
117L LEU* 1.3 72.7 - - - +
119L LEU* 1.3 61.1 + - - +
143L LYS* 3.6 22.8 + - - +
144L PHE 3.5 4.9 + - - -
145L ILE* 3.7 22.9 - - - +
321L PRO* 4.8 6.2 - - - +
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Residues in contact with LEU 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L ASN* 3.4 30.5 - - + +
106L THR 5.1 0.9 - - - +
107L VAL* 5.1 2.5 - - + -
117L LEU* 3.8 35.9 - - + +
118L SER* 1.3 76.8 - - - +
120L ASP* 1.3 65.3 + - - +
123L THR* 3.7 16.8 - - + -
124L TYR* 4.2 14.8 - - + +
127L THR* 3.9 24.7 - - + +
129L LEU* 5.5 2.7 - - + -
143L LYS* 3.5 9.3 - - - -
144L PHE* 2.7 40.8 + - - +
146L VAL* 4.9 11.9 - - + -
175L LEU* 4.8 5.6 - - + -
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Residues in contact with ASP 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J ALA* 3.5 25.4 + - + +
3J VAL* 5.4 3.3 - - - +
103L GLU 4.7 8.4 - - - +
104L ASP* 5.0 4.0 - - - +
105L ASN* 2.9 14.1 + - - +
119L LEU* 1.3 76.1 - - - +
121L LYS* 1.3 59.6 + - - +
122L ASP* 3.9 15.5 - - - +
123L THR* 2.9 27.9 + - - -
124L TYR* 3.1 28.1 + - - +
142L MET 3.4 9.2 - - - +
143L LYS* 3.5 13.4 - - + +
144L PHE* 4.7 1.6 - - - -
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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