Contacts of the strand formed by residues 109 - 116 (chain C) in PDB entry 3NJ0
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 VAL 109 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 5.6 0.2 - - + -
25C TYR* 3.8 45.3 - - + -
51C TRP* 3.4 5.2 - - - -
102C PHE* 3.9 18.1 - - + -
103C VAL* 3.3 3.8 - - - -
104C ASP* 2.8 32.2 + - + -
107C HIS* 3.7 12.3 - - + +
108C ARG* 1.3 82.0 - - - +
110C LEU* 1.3 63.1 + - - +
127C VAL* 3.8 19.1 - - + -
128C THR 3.2 10.3 - - - +
129C SER* 3.7 17.5 - - - -
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C TRP* 4.0 5.4 - - + -
54C ILE* 3.4 43.7 - - + +
55C ARG* 3.9 19.5 - - - +
57C PHE* 5.0 6.7 - - + -
63C TYR* 6.0 0.9 - - - +
83C ARG* 6.1 0.2 - - - +
100C LEU* 3.5 30.1 - - + -
102C PHE 3.4 4.9 - - - +
103C VAL* 4.3 8.5 - - + -
109C VAL* 1.3 78.0 - - - +
111C SER* 1.3 70.7 + - - +
112C PHE* 4.2 17.0 - - + -
126C SER 4.1 0.3 - - - +
127C VAL* 3.5 1.7 - - - +
128C THR* 2.9 36.8 + - - +
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Residues in contact with SER 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C LEU* 3.5 5.4 - - - +
101C GLU* 2.8 30.7 + - - +
102C PHE* 2.9 30.9 + - - -
110C LEU* 1.3 78.7 - - - +
112C PHE* 1.3 65.9 + - - +
125C LYS* 5.8 1.0 - - - +
126C SER 3.2 14.6 + - - -
127C VAL* 3.7 19.9 - - - +
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Residues in contact with PHE 112 (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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57C PHE* 4.1 11.7 - - + -
63C TYR* 5.6 3.1 - - - -
64C LYS* 3.7 18.8 - - - -
83C ARG* 3.9 13.2 - - - -
98C GLU* 3.8 28.7 - - + -
99C ARG 3.2 18.6 - - - +
101C GLU* 4.1 5.2 - - - -
110C LEU* 4.2 15.0 - - + -
111C SER* 1.3 77.5 + - - +
113C ARG* 1.3 70.9 + - - +
114C VAL* 4.8 0.4 - - + -
124C TYR* 4.0 13.7 - + - -
125C LYS* 3.4 4.9 - - - +
126C SER* 3.0 55.7 + - - +
128C THR* 5.8 1.8 - - - -
147C GLU* 4.8 3.1 - - - -
300C PYV 3.6 30.1 - - - -
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Residues in contact with ARG 113 (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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186B MET* 3.8 39.7 + - - +
187B HIS 4.2 14.9 + - - -
98C GLU* 3.4 2.1 - - - -
99C ARG 2.9 27.3 + - - +
101C GLU* 3.2 37.2 + - + +
112C PHE* 1.3 83.0 - - - +
114C VAL* 1.3 71.7 + - - +
115C VAL* 3.6 8.4 + - + +
123C ASN* 5.2 5.7 + - - -
124C TYR 3.5 5.8 - - - +
125C LYS* 3.6 48.1 - - + +
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Residues in contact with VAL 114 (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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96C SER* 3.9 6.3 - - - +
97C THR 3.5 7.2 - - - +
98C GLU* 4.1 10.3 - - + -
112C PHE* 4.8 0.7 - - + -
113C ARG* 1.3 82.8 + - - +
115C VAL* 1.3 64.1 + - - +
116C GLY 3.5 20.2 - - - +
119C HIS* 3.6 23.6 - - + +
121C LEU 6.0 0.2 - - - +
123C ASN* 4.9 12.2 - - - +
124C TYR* 2.8 44.8 + - + +
300C PYV 3.8 25.6 - - + +
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Residues in contact with VAL 115 (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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48B SER* 3.8 35.2 - - - +
49B VAL* 4.6 8.5 - - + -
186B MET* 4.0 21.1 - - + -
82C VAL* 5.5 1.1 - - + -
97C THR* 2.8 23.0 + - + +
98C GLU 4.8 0.4 - - - -
99C ARG* 3.8 32.8 - - + +
113C ARG* 4.0 5.6 - - + +
114C VAL* 1.3 79.3 - - - +
116C GLY* 1.3 57.4 + - - +
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Residues in contact with GLY 116 (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 THR 4.8 3.4 - - - -
96C SER* 3.8 2.0 - - - -
97C THR* 2.9 39.5 + - - -
114C VAL* 3.5 3.8 - - - +
115C VAL* 1.3 81.7 - - - +
119C HIS* 3.2 32.0 + - - -
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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