Contacts of the helix formed by residues 94 - 104 (chain L) in PDB entry 4XLN
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 ASP 94 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92L THR 3.6 2.5 - - - +
93L SER* 1.3 73.3 - - - +
95L PRO* 1.3 72.3 - - - +
96L VAL* 2.8 45.3 + - - +
97L ARG* 2.7 45.8 + - + +
98L GLN* 3.4 21.4 + - - +
32R G 4.1 5.9 + - - -
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Residues in contact with PRO 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572J ARG* 4.1 15.8 + - + -
576J GLU* 3.9 26.7 - - - +
587J ARG* 4.9 11.0 - - - +
93L SER 3.5 8.7 - - - +
94L ASP* 1.3 91.2 - - - +
96L VAL* 1.3 67.5 + - + +
97L ARG 3.5 0.2 - - - -
98L GLN* 3.4 17.8 - - + +
99L TYR 3.6 4.5 + - - -
225L LEU* 3.7 23.3 - - + +
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Residues in contact with VAL 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L ASP* 2.8 26.0 + - - +
95L PRO* 1.3 75.0 - - + +
97L ARG* 1.3 61.5 + - - +
98L GLN 3.1 2.2 - - - -
99L TYR* 3.3 3.9 + - - +
100L LEU* 2.9 35.2 + - + +
224L PHE* 4.6 16.6 - - + -
225L LEU* 3.5 25.4 - - + -
32R G 3.2 51.1 - - + +
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Residues in contact with ARG 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243I ARG* 3.2 24.4 - - - +
245I GLY* 3.6 36.1 + - - +
94L ASP* 2.7 46.5 + - + +
95L PRO 3.5 0.2 - - - -
96L VAL* 1.3 78.4 - - - +
98L GLN* 1.3 59.5 + - - +
100L LEU* 3.7 9.7 - - + +
101L HIS* 2.9 35.0 + - + +
31R G 4.5 1.6 + - - +
32R G 2.9 35.6 + - - +
33R G 2.9 42.6 + - - +
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Residues in contact with GLN 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J TYR* 3.7 13.7 - - - +
129J PHE 2.7 25.9 + - - -
130J ASN* 3.0 36.0 + - - +
568J ARG* 5.0 0.4 - - - +
572J ARG* 3.4 26.8 - - - +
93L SER 6.1 0.3 - - - -
94L ASP 3.4 12.5 + - - +
95L PRO* 3.4 13.7 - - - +
97L ARG* 1.3 80.2 - - - +
99L TYR* 1.3 56.9 + - - +
101L HIS* 3.8 1.8 - - - +
102L GLU* 2.9 43.8 + - + +
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Residues in contact with TYR 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565J ILE* 4.0 17.9 - - + -
566J ILE* 3.7 9.9 - - - +
569J ASN* 3.1 44.6 - - + +
572J ARG* 4.2 2.9 - - - +
95L PRO 3.6 5.9 + - - +
96L VAL* 3.3 7.9 + - - +
98L GLN* 1.3 77.7 - - - +
100L LEU* 1.3 61.7 + - + +
102L GLU* 3.1 8.8 + - - +
103L ILE* 2.9 38.9 + - + +
207L LEU* 3.1 41.9 - - + +
211L VAL* 4.0 11.7 - - + -
225L LEU* 4.8 8.5 - - + -
228L ILE* 3.9 27.6 - - + -
229L GLN* 3.8 9.1 + - + -
232L ASN* 3.6 10.6 + - - -
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Residues in contact with LEU 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245I GLY 6.0 0.9 - - - +
96L VAL* 2.9 32.5 + - + +
97L ARG* 3.7 8.1 - - + +
98L GLN 3.3 0.2 - - - -
99L TYR* 1.3 77.6 - - + +
101L HIS* 1.3 56.5 + - - +
103L ILE* 3.2 11.5 - - + +
104L GLY 3.1 19.2 + - - -
211L VAL* 4.1 18.6 - - + -
31R G 3.3 62.0 - - - +
32R G 3.2 45.3 - - + +
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Residues in contact with HIS 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245I GLY 4.8 9.2 - - - -
246I ASP* 4.5 2.4 + - - -
247I PRO* 3.7 27.3 - - + +
97L ARG* 2.9 19.3 + - + +
98L GLN* 4.2 1.8 - - - +
100L LEU* 1.3 74.8 - - - +
102L GLU* 1.3 62.8 + - - +
103L ILE 3.4 0.2 - - - -
104L GLY 3.3 6.5 + - - -
105L GLN* 2.8 41.7 + - - +
31R G 3.1 34.4 + - - +
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Residues in contact with GLU 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565J ILE* 3.9 36.8 - - + +
568J ARG* 2.9 35.1 + - - +
569J ASN 5.1 0.3 + - - -
572J ARG* 3.6 18.4 + - - -
98L GLN* 2.9 42.1 + - + +
99L TYR* 3.1 9.8 + - + +
101L HIS* 1.3 80.9 - - - +
103L ILE* 1.3 59.4 + - - +
104L GLY 3.5 0.2 + - - -
105L GLN* 3.6 17.2 + - - +
106L VAL* 4.5 5.0 + - - +
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Residues in contact with ILE 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565J ILE* 5.0 2.9 - - + -
99L TYR* 2.9 28.0 + - + +
100L LEU* 3.2 17.5 - - - +
102L GLU* 1.3 73.5 - - + +
104L GLY* 1.3 54.1 + - - +
105L GLN 3.1 5.8 + - - -
106L VAL* 3.3 17.2 + - - +
204L GLU 5.5 2.2 - - - +
207L LEU* 3.7 35.9 - - + -
208L ARG* 2.7 47.4 + - + +
211L VAL* 3.6 26.7 - - + -
31R G 3.7 22.2 - - + +
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Residues in contact with GLY 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L LEU 3.1 9.1 + - - -
101L HIS* 3.3 5.4 + - - -
102L GLU 3.2 1.0 - - - -
103L ILE* 1.3 77.4 - - - +
105L GLN* 1.3 66.5 + - - +
106L VAL 3.5 1.7 - - - +
107L PRO* 5.1 1.0 - - - +
208L ARG* 3.3 16.4 + - - -
31R G 3.6 32.6 - - - +
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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