Contacts of the helix formed by residues 94 - 106 (chain C) in PDB entry 3LL8
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 GLN 94 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C ILE* 3.3 15.1 + - + +
92C HIS* 3.1 9.6 - - - +
93C GLY* 1.3 75.5 - - - +
95C PHE* 1.3 59.6 + - - +
96C PHE 3.3 2.9 - - - -
97C ASP* 2.8 35.9 + - + +
98C LEU* 3.0 24.4 + - - +
123C GLY* 4.6 8.0 + - - -
125C PHE* 5.1 2.5 - - - -
129C CYS* 3.9 3.2 - - - -
308C ALA* 3.6 19.8 - - + +
309C PRO* 3.0 30.1 + - - +
310C ASN 4.7 1.7 + - - -
311C TYR* 3.7 24.3 - - - -
312C LEU* 3.8 5.5 + - - +
313C ASP* 6.0 1.6 - - - -
339C HIS* 6.4 3.1 - - + -
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Residues in contact with PHE 95 (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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47C LYS* 4.7 2.7 - - - -
50C LEU* 3.8 29.6 - - + -
51C MET* 3.8 26.9 - - + -
93C GLY 3.2 4.4 + - - -
94C GLN* 1.3 75.4 - - - +
96C PHE* 1.3 74.5 + + + +
98C LEU* 3.2 6.1 + - + +
99C MET* 3.0 58.1 + - + +
125C PHE* 3.5 26.6 - - + +
128C GLU* 3.4 39.9 - - + -
129C CYS* 3.6 15.7 - - - -
132C TYR* 3.7 15.0 - + + -
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Residues in contact with PHE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU 4.4 4.7 - - - -
51C MET* 3.3 62.1 - - + -
53C GLU* 4.8 2.5 - - + -
94C GLN 3.3 1.2 - - - -
95C PHE* 1.3 82.2 - + - +
97C ASP* 1.3 62.8 + - - +
99C MET* 3.6 8.7 + - - +
100C LYS* 3.5 12.6 + - - +
125C PHE* 3.9 29.8 - + - -
337C SER* 4.0 16.7 + - - +
338C PRO 3.5 24.2 - - - +
339C HIS* 3.6 19.3 - - + -
340C PRO* 3.4 28.9 - - + -
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Residues in contact with ASP 97 (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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91C ILE* 6.2 0.2 - - - -
94C GLN* 2.8 38.0 + - + +
96C PHE* 1.3 74.4 - - - +
98C LEU* 1.3 59.7 + - - +
99C MET 3.2 1.8 - - - -
100C LYS* 3.1 8.7 + - - +
101C LEU* 2.8 27.3 + - - +
307C SER 5.1 2.2 - - - +
309C PRO* 3.4 33.7 - - + +
334C PHE* 3.8 5.3 - - + -
335C ASN 4.5 0.3 - - - +
336C CYS* 3.4 5.9 - - - +
337C SER* 2.9 35.9 + - - +
339C HIS* 5.5 5.6 - - - -
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ILE* 4.0 23.4 - - + +
94C GLN 3.0 12.9 + - - +
95C PHE* 3.2 11.6 + - + +
97C ASP* 1.3 74.2 - - - +
99C MET* 1.3 74.6 + - + +
101C LEU* 3.2 11.3 + - + +
102C PHE* 3.1 52.9 + - + -
115C PHE* 3.9 26.0 - - + -
129C CYS* 4.3 22.7 - - - -
132C TYR* 4.3 5.8 - - + -
133C LEU* 4.1 24.5 - - + -
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Residues in contact with MET 99 (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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47C LYS* 3.8 40.6 + - - +
51C MET* 3.9 26.5 - - + -
95C PHE* 3.0 50.8 + - + +
96C PHE* 3.7 9.6 - - - +
97C ASP 3.2 0.2 - - - -
98C LEU* 1.3 87.3 - - + +
100C LYS* 1.3 61.7 + - - +
102C PHE* 3.5 6.4 + - + +
103C GLU* 3.4 22.4 + - - +
132C TYR* 3.5 35.7 - - + -
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Residues in contact with LYS 100 (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 PHE 3.5 4.4 + - - +
97C ASP* 3.1 9.9 + - - +
99C MET* 1.3 75.8 - - - +
101C LEU* 1.3 68.4 + - - +
103C GLU* 3.0 30.5 + - + +
104C VAL* 2.9 35.4 + - - +
334C PHE* 3.8 28.0 - - + -
335C ASN 4.4 7.9 - - - +
337C SER* 3.9 22.4 - - - +
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Residues in contact with LEU 101 (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 CYS* 3.9 9.9 - - - -
91C ILE* 3.7 31.0 - - + -
97C ASP 2.8 12.8 + - - +
98C LEU* 3.3 14.6 - - + +
100C LYS* 1.3 76.1 - - - +
102C PHE* 1.3 59.2 + - + +
104C VAL* 3.1 4.3 + - - +
105C GLY 2.7 31.9 + - - -
113C TYR* 3.8 25.8 - - + -
115C PHE* 4.0 15.5 - - + -
307C SER* 3.8 18.6 - - - +
321C VAL* 3.8 17.8 - - + +
334C PHE* 3.8 19.9 - - + -
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Residues in contact with PHE 102 (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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98C LEU* 3.1 43.9 + - + -
99C MET* 3.9 7.6 - - + +
100C LYS 3.2 0.2 - - - -
101C LEU* 1.3 75.8 - - + +
103C GLU* 1.3 65.8 + - - +
106C GLY* 2.9 26.7 + - - +
107C SER* 4.1 1.4 + - - -
108C PRO* 3.7 29.4 - - + -
113C TYR* 3.5 39.3 - + - -
115C PHE* 3.7 21.8 - + - -
132C TYR* 3.9 17.7 - + - +
133C LEU* 4.0 4.5 - - + -
136C LEU* 3.6 26.5 - - + -
144C LEU* 4.5 2.0 - - + -
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Residues in contact with GLU 103 (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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47C LYS* 4.9 11.2 + - - +
99C MET 3.4 12.9 + - - +
100C LYS* 3.0 36.9 + - + +
102C PHE* 1.3 80.3 - - - +
104C VAL* 1.3 61.7 + - + +
106C GLY* 3.7 5.2 + - - -
332C ARG* 5.1 0.3 + - - -
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Residues in contact with VAL 104 (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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100C LYS* 2.9 30.0 + - - +
101C LEU 3.6 6.5 - - - +
103C GLU* 1.3 75.0 - - - +
105C GLY* 1.3 65.2 + - - +
106C GLY 3.6 0.2 + - - -
321C VAL* 4.2 10.8 - - + -
323C LYS* 4.3 3.5 - - - +
332C ARG* 2.6 76.8 + - + +
333C GLN 4.8 2.5 - - - +
334C PHE* 3.8 31.2 - - + -
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Residues in contact with GLY 105 (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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86C THR* 3.8 14.1 + - - -
101C LEU 2.7 16.2 + - - -
104C VAL* 1.3 76.2 - - - +
106C GLY* 1.3 56.5 + - - +
111C THR* 3.6 8.5 - - - +
113C TYR* 3.1 16.8 - - - -
321C VAL* 4.5 4.5 - - - +
323C LYS* 2.9 33.5 + - - -
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Residues in contact with GLY 106 (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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102C PHE* 2.9 16.0 + - - +
103C GLU 3.7 4.8 + - - -
104C VAL 3.3 3.0 - - - -
105C GLY* 1.3 79.8 - - - +
107C SER* 1.3 68.2 + - - -
108C PRO* 3.4 2.1 - - - +
110C ASN* 5.1 0.9 - - - -
111C THR* 3.3 8.3 - - - -
113C TYR* 2.5 26.0 + - - -
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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