Contacts of the helix formed by residues 91 - 107 (chain C) in PDB entry 2FVL
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 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C THR 5.5 0.2 + - - -
89C PHE 3.3 0.6 - - - -
90C PHE* 1.3 77.4 - - - +
92C PRO* 1.3 63.7 - - + +
93C GLN* 2.8 38.1 + - - +
94C MET* 2.8 38.3 + - + +
95C VAL* 3.5 3.3 + - - +
124C PRO* 3.4 25.3 - - + +
140C ASP* 2.9 25.8 + - - +
142C VAL* 3.7 19.3 - - + +
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Residues in contact with PRO 92 (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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90C PHE 3.4 5.1 - - - +
91C GLN* 1.3 85.1 - - + -
93C GLN* 1.3 66.2 + - - +
94C MET 3.2 1.0 + - - -
95C VAL* 3.3 14.1 + - + -
96C GLN 4.6 0.7 + - - -
142C VAL* 4.2 10.8 - - + -
146C ALA* 3.8 28.5 - - + +
150C VAL* 3.7 38.0 - - + +
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Residues in contact with GLN 93 (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 GLN* 2.8 41.6 + - - +
92C PRO* 1.3 80.8 - - - +
94C MET* 1.3 69.1 + - + +
97C PRO* 3.5 21.2 - - - +
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Residues in contact with MET 94 (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 THR 3.9 16.8 - - - +
89C PHE* 3.6 41.1 - - + +
91C GLN* 2.8 23.0 + - + +
93C GLN* 1.3 95.2 - - + +
95C VAL* 1.3 60.8 + - - +
96C GLN 3.6 1.1 - - - -
97C PRO* 3.6 7.1 - - - +
98C ALA* 3.2 24.6 + - - +
124C PRO* 4.0 22.2 - - + -
125C GLY 5.4 3.4 - - - +
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Residues in contact with VAL 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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85C LEU* 3.9 27.4 - - + +
89C PHE 3.5 16.8 - - - +
90C PHE 4.0 2.2 - - - +
91C GLN 3.7 10.1 - - - +
92C PRO* 3.3 10.3 + - + +
94C MET* 1.3 76.0 - - - +
96C GLN* 1.3 64.0 + - - +
98C ALA* 3.3 5.2 + - - +
99C LEU* 3.2 20.3 + - - +
114C TYR* 4.9 0.9 - - + -
147C THR* 4.0 16.6 - - + -
150C VAL* 3.6 28.3 - - + -
151C MET* 4.0 22.9 - - + +
154C CYS* 4.4 6.1 - - - -
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Residues in contact with GLN 96 (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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92C PRO 4.6 0.4 + - - -
95C VAL* 1.3 80.0 - - - +
97C PRO* 1.3 63.8 - - + +
99C LEU* 3.2 2.9 + - - +
100C GLU* 2.9 49.2 + - - +
150C VAL* 4.0 8.7 - - + +
153C LYS* 3.0 41.1 + - - +
154C CYS* 4.0 23.4 - - - -
157C ALA* 4.8 8.4 - - - +
159C LEU* 4.0 17.9 - - + +
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Residues in contact with PRO 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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93C GLN 3.5 25.6 - - - +
94C MET* 3.6 8.7 - - - +
96C GLN* 1.3 95.6 - - + +
98C ALA* 1.3 55.3 + - - +
100C GLU* 3.8 14.1 - - + +
101C SER* 2.9 29.6 + - - -
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Residues in contact with ALA 98 (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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85C LEU* 3.3 31.2 - - + -
89C PHE* 4.0 22.4 - - + -
94C MET 3.2 13.9 + - - +
95C VAL 3.4 0.7 - - - +
96C GLN 3.2 0.6 - - - -
97C PRO* 1.3 74.7 - - - +
99C LEU* 1.3 66.2 + - - +
101C SER* 3.3 7.1 + - - -
102C SER* 3.1 25.1 + - - -
114C TYR* 3.6 3.8 - - - +
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Residues in contact with LEU 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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95C VAL 3.2 7.2 + - - +
96C GLN 3.5 7.6 - - - +
98C ALA* 1.3 80.1 - - - +
100C GLU* 1.3 62.6 + - - +
102C SER* 3.1 6.0 + - - -
103C LEU* 3.0 38.0 + - + +
111C VAL* 4.1 17.3 - - + -
114C TYR* 3.4 48.1 + - + -
154C CYS* 3.6 35.9 - - + -
159C LEU* 3.8 23.6 - - + +
160C ALA* 4.4 3.8 - - + -
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Residues in contact with GLU 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 GLN* 2.9 48.9 + - - +
97C PRO* 3.8 11.1 - - + +
99C LEU* 1.3 75.5 - - - +
101C SER* 1.3 58.6 + - - +
103C LEU* 3.8 10.5 - - + +
104C LYS* 3.0 27.9 + - - +
159C LEU* 4.1 19.5 - - + +
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Residues in contact with SER 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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53C TYR* 5.9 2.8 - - - -
97C PRO 2.9 19.9 + - - -
98C ALA* 3.5 8.3 - - - -
99C LEU 3.1 0.2 - - - -
100C GLU* 1.3 74.0 - - - +
102C SER* 1.3 65.4 + - - +
104C LYS* 3.5 11.3 + - - +
105C LYS* 3.2 36.0 + - - +
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Residues in contact with SER 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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53C TYR* 4.6 12.0 - - - +
58C GLU* 2.8 34.5 + - - +
83C SER* 3.9 10.4 + - - -
84C LYS 5.3 0.5 + - - -
98C ALA 3.1 11.7 + - - -
99C LEU* 3.1 14.6 + - - -
101C SER* 1.3 75.0 + - - +
103C LEU* 1.3 59.8 + - - +
105C LYS* 3.1 7.2 + - - +
106C LEU* 2.9 37.4 + - - +
111C VAL* 5.7 0.2 - - - -
114C TYR* 4.6 5.1 + - - -
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Residues in contact with LEU 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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99C LEU* 3.0 26.0 + - + +
100C GLU* 3.8 10.3 - - + +
102C SER* 1.3 76.2 - - - +
104C LYS* 1.3 52.6 + - - +
106C LEU* 4.0 7.0 - - + -
107C GLN* 2.7 30.7 + - - -
108C LEU* 3.2 23.4 + - + +
109C ASP 3.8 16.8 - - - +
110C TYR* 3.5 32.1 - - - +
111C VAL* 3.6 19.5 - - + +
159C LEU* 3.9 32.8 - - + +
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Residues in contact with LYS 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 GLU 3.0 18.3 + - - +
101C SER* 3.6 10.8 - - - +
102C SER 3.2 0.4 - - - -
103C LEU* 1.3 78.3 - - - +
105C LYS* 1.3 61.1 + - + +
107C GLN* 3.5 19.1 + - - +
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Residues in contact with LYS 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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53C TYR* 6.4 2.7 - - + -
58C GLU* 4.2 11.9 - - + +
59C GLU* 3.4 59.6 + - - +
66C ARG* 5.4 0.9 + - - -
101C SER* 3.2 23.9 + - - +
102C SER* 3.1 11.7 + - - +
104C LYS* 1.3 77.3 - - + +
106C LEU* 1.3 61.6 + - - +
107C GLN* 3.6 7.4 + - - +
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Residues in contact with LEU 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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58C GLU* 3.2 35.7 - - + +
61C VAL* 4.8 0.4 - - + -
62C GLY* 3.7 21.0 - - - +
65C ILE* 5.4 0.2 - - + -
66C ARG* 3.0 24.4 + - - -
81C TYR* 3.5 49.8 - - + +
102C SER* 2.9 29.6 + - - +
103C LEU* 3.7 11.2 - - + +
105C LYS* 1.3 76.4 - - - +
107C GLN* 1.3 60.3 - - - +
108C LEU* 3.5 20.6 + - + +
111C VAL* 4.3 10.5 - - + -
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Residues in contact with GLN 107 (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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59C GLU* 6.1 2.2 - - - +
66C ARG* 3.4 45.6 + - - +
103C LEU 2.7 14.6 + - - -
104C LYS* 3.5 15.0 + - - +
105C LYS 3.3 5.5 + - - +
106C LEU* 1.3 77.2 - - - +
108C LEU* 1.3 58.4 + - - +
109C ASP* 5.4 1.0 - - - +
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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