Contacts of the helix formed by residues 87 - 104 (chain U) in PDB entry 6FF7
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 87 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85U VAL 3.3 7.0 + - - -
86U SER* 1.3 76.7 - - - +
88U LYS* 1.3 67.0 + - - +
89U ALA* 3.3 9.0 - - - -
90U TYR* 3.5 10.6 - - - +
91U LEU* 3.0 23.1 + - - +
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Residues in contact with LYS 88 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87U SER* 1.3 72.4 - - - +
89U ALA* 1.3 65.6 - - - +
91U LEU* 3.1 7.5 + - - +
92U MET* 2.9 26.4 + - - +
137U GLU* 6.5 0.9 - - + -
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Residues in contact with ALA 89 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46U ILE* 4.3 4.4 - - + +
47U GLU* 4.2 22.0 - - + +
50U TYR* 3.8 26.6 - - + +
87U SER* 3.3 5.5 - - - -
88U LYS* 1.3 78.1 - - - +
90U TYR* 1.3 57.5 + - - +
92U MET* 4.1 4.7 - - - +
93U SER* 3.0 31.7 + - - -
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Residues in contact with TYR 90 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46U ILE* 5.4 11.0 - - + +
77U LEU* 6.0 1.0 - - - +
85U VAL 4.5 4.3 - - - +
86U SER* 4.4 7.4 - - - -
87U SER* 3.2 26.0 + - - +
88U LYS 3.1 0.6 - - - -
89U ALA* 1.3 78.0 - - - +
91U LEU* 1.3 65.2 + - - +
93U SER* 3.5 4.6 + - - -
94U ILE* 3.2 23.2 + - - +
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Residues in contact with LEU 91 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87U SER 3.0 16.5 + - - +
88U LYS* 3.6 6.1 - - - +
90U TYR* 1.3 77.4 - - - +
92U MET* 1.3 63.9 + - - +
94U ILE* 3.4 5.3 + - - +
95U CYS* 3.2 21.5 + - - +
122U PHE 6.1 0.7 - - - +
125U HIS* 5.7 10.1 - - + +
126U ILE* 5.9 5.4 - - + -
129U ALA* 5.9 5.6 - - + -
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Residues in contact with MET 92 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50U TYR* 6.1 1.8 - - + -
88U LYS 2.9 17.9 + - - +
89U ALA* 4.1 5.2 - - - +
91U LEU* 1.3 76.4 - - - +
93U SER* 1.3 58.4 + - - +
95U CYS* 3.2 7.7 + - - +
96U CYS* 2.8 30.2 + - - +
142U GLU* 6.0 6.3 - - + -
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Residues in contact with SER 93 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46U ILE* 5.7 7.0 - - - -
50U TYR* 5.2 8.0 - - - +
77U LEU* 5.7 7.4 - - - -
89U ALA 3.0 21.0 + - - -
90U TYR* 3.8 6.1 - - - -
91U LEU 3.3 0.2 - - - -
92U MET* 1.3 75.7 - - - +
94U ILE* 1.3 62.9 + - - +
96U CYS* 3.4 7.4 + - - +
97U MET* 3.1 22.7 + - - +
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Residues in contact with ILE 94 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73U LEU* 6.1 1.3 - - - -
77U LEU* 5.3 13.8 - - + +
78U TRP* 6.6 0.9 - - + -
90U TYR 3.2 10.0 + - - +
91U LEU* 3.7 10.1 - - - +
93U SER* 1.3 79.5 - - - +
95U CYS* 1.3 56.2 + - - +
97U MET* 3.3 7.2 + - - +
98U VAL* 3.0 28.5 + - - +
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Residues in contact with CYS 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91U LEU 3.2 11.7 + - - +
92U MET* 3.2 10.1 + - - +
94U ILE* 1.3 77.8 - - - +
96U CYS* 1.3 60.0 + - - +
98U VAL* 3.9 5.9 - - - +
99U ASN* 2.9 31.7 + - - +
145U VAL* 5.0 12.5 - - + +
146U LEU* 5.5 2.2 - - - -
149U PHE* 4.2 24.0 - - + +
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Residues in contact with CYS 96 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U ILE* 6.4 2.0 - - + -
64U ILE* 5.5 10.6 - - + +
92U MET 2.8 17.1 + - - +
93U SER* 3.7 8.3 - - - +
95U CYS* 1.3 75.7 - - - +
97U MET* 1.3 58.8 + - - +
99U ASN* 3.5 5.4 + - - +
100U GLU* 2.9 29.6 + - - +
145U VAL* 6.1 4.2 - - + +
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Residues in contact with MET 97 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U GLU* 5.0 14.8 - - + +
72U TYR* 6.0 2.5 - - + -
73U LEU* 3.8 31.6 - - + +
93U SER 3.1 16.0 + - - +
94U ILE* 3.6 5.6 - - - +
96U CYS* 1.3 75.1 - - - +
98U VAL* 1.3 65.2 + - - +
100U GLU* 3.3 6.4 + - - +
101U LYS* 3.0 23.4 + - - +
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Residues in contact with VAL 98 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94U ILE 3.0 17.6 + - - +
95U CYS* 3.9 6.7 - - - +
96U CYS 3.4 0.2 - - - -
97U MET* 1.3 74.7 - - - +
99U ASN* 1.3 63.1 + - - +
101U LYS* 3.2 9.4 + - - +
102U PHE* 3.2 20.3 + - - +
108U ALA* 4.2 21.3 - - + +
149U PHE* 6.0 3.8 - - + -
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Residues in contact with ASN 99 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95U CYS 2.9 19.1 + - - +
96U CYS* 3.8 5.8 - - - +
98U VAL* 1.3 76.2 - - - +
100U GLU* 1.3 57.5 + - - +
102U PHE* 3.2 9.2 + - - +
103U ARG* 3.0 26.0 + - - +
145U VAL* 5.5 7.9 - - + +
148U LEU* 5.5 10.1 - - + -
149U PHE* 5.6 6.9 - - - +
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Residues in contact with GLU 100 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64U ILE* 4.8 16.2 - - + +
65U MET* 5.7 1.8 - - - -
68U GLU* 4.4 19.1 - - + -
96U CYS 2.9 18.8 + - - +
97U MET* 3.7 5.8 - - - +
99U ASN* 1.3 73.0 - - - +
101U LYS* 1.3 61.4 + - - +
103U ARG* 3.1 10.5 + - - +
104U GLU* 2.9 29.9 + - - +
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Residues in contact with LYS 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U GLU* 5.5 2.8 - - + +
97U MET 3.0 13.4 + - - +
98U VAL* 3.2 11.0 + - - +
100U GLU* 1.3 76.0 - - - +
102U PHE* 1.3 57.4 + - - +
104U GLU* 3.3 4.9 + - - +
105U ASN 2.9 21.8 + - - -
106U VAL* 3.0 31.7 + - + +
107U PRO 4.3 3.8 - - - +
108U ALA* 4.0 17.0 - - + -
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Residues in contact with PHE 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98U VAL 3.2 12.0 + - - +
99U ASN* 3.4 11.0 - - - +
100U GLU 3.2 0.2 - - - -
101U LYS* 1.3 75.2 - - - +
103U ARG* 1.3 65.6 + - - +
105U ASN* 3.1 14.9 + - - +
106U VAL 5.0 1.3 - - - -
108U ALA* 4.8 6.2 - - + +
152U HIS* 5.5 11.4 - - + -
1111U LYS 4.9 7.6 - - - +
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Residues in contact with ARG 103 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99U ASN 3.0 12.6 + - - +
100U GLU* 3.1 14.1 + - - +
102U PHE* 1.3 76.1 - - - +
104U GLU* 1.3 58.9 + - + +
105U ASN* 3.7 0.9 + - - +
445U SER 5.0 12.3 - - - +
446U GLY* 4.9 16.0 - - - +
1111U LYS* 4.9 15.1 - - - +
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Residues in contact with GLU 104 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100U GLU 2.9 15.6 + - - +
101U LYS* 4.0 5.6 - - - +
102U PHE 3.1 0.2 - - - -
103U ARG* 1.3 75.7 - - + +
105U ASN* 1.3 70.8 + - - +
106U VAL* 3.4 7.8 + - + +
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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