Contacts of the helix formed by residues 4 - 21 (chain 1) 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 LEU 4 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21 ASN 4.4 1.0 - - - +
31 PRO* 1.3 79.6 - - + +
51 THR* 1.3 65.7 + - - +
61 LYS* 3.2 3.6 - - - +
71 VAL* 3.4 24.6 - - + +
81 LYS* 4.0 2.4 + - - +
1061 THR* 5.5 14.4 - - - +
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Residues in contact with THR 5 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21 ASN* 4.0 22.5 - - - +
31 PRO 3.8 0.2 - - - -
41 LEU* 1.3 76.9 - - - +
61 LYS* 1.3 59.0 + - - +
71 VAL 3.2 1.3 - - - -
81 LYS* 3.1 12.9 + - - +
91 LEU* 2.9 24.3 + - - +
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Residues in contact with LYS 6 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21 ASN 4.9 6.0 + - - +
31 PRO 5.6 2.7 - - - +
41 LEU* 3.2 2.4 - - - +
51 THR* 1.3 76.4 - - - +
71 VAL* 1.3 60.1 + - - +
91 LEU* 3.6 10.1 - - + +
101 ILE* 2.9 31.5 + - - +
1081 ARG* 5.5 6.3 - - + -
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Residues in contact with VAL 7 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41 LEU* 3.4 20.5 + - + +
51 THR 3.2 0.2 - - - -
61 LYS* 1.3 78.2 - - - +
81 LYS* 1.3 56.7 + - - +
101 ILE* 3.5 4.4 + - - +
111 ASN* 2.9 30.4 + - - +
981 ASN* 5.7 6.2 - - + +
991 GLY* 5.2 14.1 - - - +
1061 THR* 6.2 3.1 - - - -
1071 ILE 4.9 12.6 - - - +
1081 ARG* 4.9 13.3 - - + +
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Residues in contact with LYS 8 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41 LEU 4.0 1.3 + - - +
51 THR* 3.1 17.9 + - - +
71 VAL* 1.3 79.0 - - - +
91 LEU* 1.3 56.5 + - - +
111 ASN* 3.4 6.5 + - - +
121 GLU* 2.9 30.0 + - - +
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Residues in contact with LEU 9 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51 THR 2.9 13.2 + - - +
61 LYS* 3.6 13.0 - - + +
71 VAL 3.3 0.6 - - - -
81 LYS* 1.3 77.0 - - - +
101 ILE* 1.3 57.7 + - - +
121 GLU* 3.2 7.0 + - - +
131 LEU* 3.0 27.5 + - - +
782u GLU* 6.1 5.4 - - + -
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Residues in contact with ILE 10 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61 LYS 2.9 16.3 + - - +
71 VAL* 4.1 3.6 - - - +
91 LEU* 1.3 75.2 - - - +
111 ASN* 1.3 61.9 + - - +
131 LEU* 3.5 9.5 + - - +
141 ASN* 3.3 19.8 + - - +
941 VAL 6.0 1.6 - - - +
981 ASN* 5.7 8.3 - - + -
1091 VAL 5.2 9.2 - - - +
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Residues in contact with ASN 11 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71 VAL 2.9 18.9 + - - +
81 LYS* 3.7 8.1 - - - +
101 ILE* 1.3 76.9 - - - +
121 GLU* 1.3 57.6 + - - +
141 ASN* 3.3 6.7 + - - +
151 GLU* 2.9 28.0 + - - +
981 ASN* 6.5 1.1 - - + -
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Residues in contact with GLU 12 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81 LYS 2.9 17.9 + - - +
91 LEU* 3.2 6.7 + - - +
111 ASN* 1.3 71.9 - - - +
131 LEU* 1.3 59.2 + - - +
151 GLU* 3.8 8.5 - - - +
161 ARG* 2.9 30.8 + - - +
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Residues in contact with LEU 13 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91 LEU 3.0 12.7 + - - +
101 ILE* 3.6 12.8 - - - +
111 ASN 3.2 0.2 - - - -
121 GLU* 1.3 76.6 - - - +
141 ASN* 1.3 58.4 + - - +
161 ARG* 3.3 6.0 + - - +
171 GLU* 2.9 27.8 + - - +
822u ARG* 6.1 5.4 - - + +
825u LEU* 5.2 14.1 - - + +
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Residues in contact with ASN 14 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101 ILE 3.3 8.9 + - - +
111 ASN* 3.3 9.4 + - - +
131 LEU* 1.3 79.1 - - - +
151 GLU* 1.3 57.2 + - - +
171 GLU* 3.3 8.6 + - - +
181 VAL* 2.9 30.0 + - - +
951 ASP* 6.2 6.3 - - + +
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Residues in contact with GLU 15 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111 ASN 2.9 17.5 + - - +
121 GLU* 3.8 9.0 - - - +
141 ASN* 1.3 76.9 - - - +
161 ARG* 1.3 56.5 + - - +
181 VAL* 3.5 4.8 + - - +
191 GLN* 2.9 30.4 + - - +
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Residues in contact with ARG 16 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121 GLU 2.9 18.1 + - - +
131 LEU* 3.3 6.3 + - - +
151 GLU* 1.3 73.6 - - - +
171 GLU* 1.3 60.5 + - - +
191 GLN* 3.8 6.0 - - - +
201 LEU* 2.9 33.1 + - - +
825u LEU* 5.1 16.2 - - + +
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Residues in contact with GLU 17 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131 LEU 2.9 17.2 + - - +
141 ASN* 3.6 8.5 - - - +
161 ARG* 1.3 78.1 - - - +
181 VAL* 1.3 57.0 + - - +
201 LEU* 4.1 0.6 - - - -
211 GLY* 3.2 21.1 + - - -
221 VAL* 3.2 29.2 + - + +
271 SER* 5.3 10.1 - - - -
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Residues in contact with VAL 18 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141 ASN 2.9 16.5 + - - +
151 GLU* 4.2 4.9 - - - +
171 GLU* 1.3 75.9 - - - +
191 GLN* 1.3 62.5 + - - +
211 GLY* 4.1 5.6 + - - -
5973 ARG* 5.8 8.3 - - + -
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Residues in contact with GLN 19 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 GLU 2.9 19.1 + - - +
161 ARG* 3.8 7.2 - - - +
171 GLU 3.2 0.2 - - - -
181 VAL* 1.3 79.0 - - - +
201 LEU* 1.3 61.2 + - - +
211 GLY* 3.3 1.1 + - - -
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Residues in contact with LEU 20 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 ARG 2.9 17.6 + - - +
171 GLU* 4.6 2.0 - - - +
191 GLN* 1.3 77.1 - - - +
211 GLY* 1.3 64.7 + - - +
221 VAL* 5.0 3.8 - - + +
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Residues in contact with GLY 21 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171 GLU 3.2 7.8 + - - -
181 VAL* 4.1 5.3 + - - -
191 GLN 3.3 3.8 - - - -
201 LEU* 1.3 80.5 - - - +
221 VAL* 1.3 61.5 + - - +
231 ALA 3.8 1.9 + - - -
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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