Contacts of the helix formed by residues 79 - 92 (chain I) in PDB entry 2B4X
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 SER 79 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I LEU* 1.3 82.6 - - - +
80I PRO* 1.3 59.8 - - - +
81I LEU* 3.0 1.1 - - - +
82I SER* 2.6 56.8 + - - -
83I ILE* 3.2 6.7 + - - +
219I ILE* 3.3 12.5 - - - +
369I HIS* 3.2 12.4 + - - -
421I ILE 3.2 12.6 + - - -
422I PHE* 3.5 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 80 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ASN* 4.8 2.0 - - - +
58I PHE* 4.6 7.9 - - + -
59I ALA* 3.3 43.1 - - + +
62I PHE* 5.8 1.1 - - + -
78I LEU* 4.1 8.2 - - + -
79I SER* 1.3 83.8 - - - +
81I LEU* 1.3 66.2 + - - +
83I ILE* 3.8 12.5 - - + +
84I SER* 2.9 28.9 + - - -
420I ILE* 4.0 11.2 - - + +
421I ILE 3.5 10.5 - - - +
423I MET* 4.0 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ASN* 4.4 21.1 - - + +
79I SER* 2.9 3.2 + - - +
80I PRO* 1.3 81.9 - - - +
82I SER* 1.3 67.8 + - - +
84I SER* 3.7 3.0 - - - -
85I THR* 2.9 38.9 + - - +
123I PHE* 4.9 0.9 - - + -
126I LEU* 4.6 7.9 - - + -
127I ASN* 6.2 0.2 - - - +
130I LEU* 3.4 34.1 - - + -
131I TYR* 4.2 11.9 - - + +
140I LEU* 5.3 1.1 - - + -
219I ILE* 4.9 5.2 - - + -
419I THR* 3.9 21.5 - - + -
420I ILE 3.7 15.0 + - - +
421I ILE* 3.6 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I SER* 2.6 37.7 + - - -
81I LEU* 1.3 78.0 - - - +
83I ILE* 1.3 63.9 + - - -
85I THR* 2.8 11.0 + - - -
86I ALA* 2.9 13.3 + - - +
144I ASN* 3.6 5.7 + - - +
217I ASN* 3.3 6.5 - - - +
218I THR* 3.0 35.7 + - - -
219I ILE* 3.7 13.6 - - - +
369I HIS* 3.5 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I PHE* 4.1 11.7 - - + -
62I PHE* 3.7 32.3 - - + -
78I LEU* 4.5 7.0 - - + -
79I SER 3.2 10.2 + - - +
80I PRO* 3.9 7.0 - - + +
82I SER* 1.3 78.5 + - - +
84I SER* 1.3 58.1 + - - +
86I ALA* 4.1 2.2 - - - -
87I PHE* 3.0 58.2 + - + +
106I PHE* 3.9 14.8 - - + -
217I ASN* 3.7 20.2 - - - +
329I PHE* 6.1 0.2 - - + -
331I LEU* 3.8 19.7 - - + -
335I LEU* 5.1 2.9 - - + -
369I HIS* 4.4 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55I ASN* 3.6 32.2 + - - +
58I PHE* 3.4 24.4 - - - +
80I PRO 2.9 19.6 + - - -
81I LEU* 3.7 4.3 - - - -
82I SER 2.9 3.6 + - - -
83I ILE* 1.3 69.9 - - - +
85I THR* 1.3 60.6 + - - -
86I ALA 3.1 1.6 - - - -
87I PHE 4.0 0.3 - - - -
88I ALA* 2.8 29.7 + - - +
106I PHE* 4.1 11.7 - - - +
108I PHE* 3.9 8.9 - - - -
123I PHE* 4.1 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I LEU* 2.9 27.4 + - - +
82I SER* 2.8 6.8 + - - -
84I SER* 1.3 74.2 - - - +
86I ALA* 1.3 65.4 + - - +
88I ALA* 3.4 6.5 - - - +
89I MET* 3.1 18.9 + - - +
123I PHE* 3.5 15.9 - - + -
127I ASN* 4.2 18.4 + - - +
131I TYR* 4.5 9.2 + - + +
142I SER* 5.1 2.0 - - - +
144I ASN* 3.7 16.2 - - - +
166I TYR* 3.6 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I SER 2.9 5.3 + - - +
83I ILE 3.3 9.9 - - - +
85I THR* 1.3 73.4 - - - +
87I PHE* 1.3 55.2 + - + +
88I ALA 2.7 3.4 + - - -
89I MET* 2.6 39.8 + - - +
90I THR* 3.2 4.5 + - - -
144I ASN* 3.9 8.5 - - + +
215I LEU* 3.7 15.7 - - + +
217I ASN* 3.6 41.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I ILE* 3.0 31.7 + - + +
86I ALA* 1.3 79.0 - - + +
88I ALA* 1.3 56.6 + - - +
90I THR* 3.9 9.9 - - - -
91I LYS* 3.0 28.5 + - - +
102I LEU* 4.0 11.0 - - + +
106I PHE* 3.2 36.5 - + + -
108I PHE* 5.3 2.5 - - - -
215I LEU* 3.5 20.2 - - + -
217I ASN* 4.2 3.1 - - - -
331I LEU* 3.9 11.9 - - + -
335I LEU* 3.1 37.9 - - + -
340I LEU* 3.8 16.4 - - + -
343I LEU* 4.8 8.3 - - + -
344I PHE* 4.4 6.3 - + - -
364I VAL* 6.5 0.2 - - + -
367I ALA* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I SER 2.8 21.6 + - - +
85I THR* 3.4 7.6 - - - +
86I ALA 2.7 3.0 + - - -
87I PHE* 1.3 73.3 - - - +
89I MET* 1.3 67.5 + - - +
91I LYS* 3.2 9.9 + - - +
92I LEU 3.1 16.8 + - - -
108I PHE* 4.3 9.0 - - + -
119I ILE* 5.6 0.9 - - + -
120I HIS* 3.3 11.2 - - + -
123I PHE* 3.7 19.3 - - + -
166I TYR* 3.6 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I THR* 3.1 10.4 + - + +
86I ALA* 2.6 17.5 + - - +
88I ALA* 1.3 75.2 - - - +
90I THR* 1.3 62.4 + - - +
92I LEU* 2.9 19.4 - - - +
144I ASN* 3.5 38.6 - - + +
145I ARG* 4.4 15.3 - - - +
146I LEU* 4.7 11.0 - - - -
158I TYR* 2.9 15.8 + - - +
162I SER* 3.2 28.0 - - - +
166I TYR* 3.3 43.7 - - + +
168I ALA* 4.2 10.3 - - + +
169I LYS 6.1 0.2 - - - +
215I LEU* 5.5 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ALA 3.2 8.6 + - - -
87I PHE* 3.9 10.1 - - - -
89I MET* 1.3 74.9 - - - +
91I LYS* 1.3 55.3 + - - +
92I LEU 2.8 15.3 + - - -
93I GLY* 3.0 13.7 + - - -
94I ALA* 3.8 3.5 + - - +
102I LEU* 5.1 1.8 - - + -
146I LEU* 4.1 20.7 - - + +
158I TYR* 3.5 11.4 + - - -
215I LEU* 3.6 26.7 - - + +
343I LEU* 4.5 29.4 - - + -
351I LEU* 4.8 15.2 - - + +
364I VAL* 4.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I MET* 4.4 4.2 - - - +
87I PHE 3.0 18.9 + - - +
88I ALA* 3.2 7.1 + - - +
90I THR* 1.3 77.6 - - - +
92I LEU* 1.3 62.5 + - - +
93I GLY 3.0 0.2 - - - -
94I ALA* 2.8 16.2 + - - +
99I LEU* 3.3 25.1 - - + +
102I LEU* 3.2 30.6 - - + +
103I MET* 3.8 17.3 - - - -
108I PHE* 4.4 11.7 - - + -
116I SER* 3.3 23.4 + - - -
119I ILE* 3.8 17.3 - - - -
120I HIS* 2.4 42.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I PRO 4.9 9.6 - - - +
17I MET* 3.6 26.7 - - + +
88I ALA 3.1 4.8 + - - -
89I MET* 2.9 18.0 + - - +
90I THR 2.8 2.0 + - - -
91I LYS* 1.3 77.0 - - - +
93I GLY* 1.3 55.8 + - - +
94I ALA 3.8 1.9 + - - +
120I HIS* 3.7 26.5 - - + +
158I TYR* 3.4 19.7 - - + -
161I ILE* 3.8 38.1 - - + -
162I SER* 4.1 16.8 - - - +
166I TYR* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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