Contacts of the helix formed by residues 99 - 112 (chain A) in PDB entry 4X4L
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU 2.9 15.5 + - - +
96A ILE 3.3 4.2 + - - -
98A ARG* 1.3 111.3 + - - +
100A ARG* 1.3 57.0 + - - +
101A LEU 3.4 2.7 - - - -
102A LEU* 3.4 15.3 + - + -
103A LEU* 2.9 35.8 + - + +
204A HIS* 2.8 36.0 + - - +
208A LEU* 3.4 6.4 - - + +
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Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ILE 3.0 8.9 + - - +
97A GLU* 3.3 22.0 + - - +
98A ARG 3.2 3.8 + - - -
99A ASP* 1.3 75.4 - - - +
101A LEU* 1.3 62.1 + - + +
103A LEU* 4.1 0.2 - - - +
104A ALA* 2.9 34.3 + - - +
119A TYR* 2.9 68.0 + - + -
120A LEU* 4.0 8.3 + - - +
123A LEU* 3.8 24.1 - - + +
124A ALA* 3.9 24.8 - - - +
127A ILE* 4.4 13.5 - - + +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 3.6 41.3 - - + +
11A VAL 4.0 14.8 - - - +
12A LEU* 4.0 21.1 - - + +
13A LEU* 6.4 1.6 - - + -
98A ARG 4.9 1.9 + - - +
99A ASP 3.4 0.6 - - - -
100A ARG* 1.3 78.1 - - + +
102A LEU* 1.3 53.6 + - - +
104A ALA* 3.9 1.6 - - - +
105A THR* 2.7 38.9 + - - -
115A TYR* 3.8 7.1 + - - +
119A TYR* 3.7 19.5 - - + +
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Residues in contact with LEU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.0 20.9 - - + +
16A LEU* 4.1 13.4 - - + +
99A ASP* 3.4 17.4 + - + +
101A LEU* 1.3 79.3 - - - +
103A LEU* 1.3 62.0 + - + +
105A THR* 3.3 2.3 + - - -
106A MET* 2.9 47.6 + - + +
204A HIS* 3.7 43.7 - - + +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE* 3.7 41.3 - - + +
99A ASP* 2.9 26.2 + - + +
102A LEU* 1.3 78.5 - - + +
104A ALA* 1.3 57.3 + - - +
106A MET* 3.3 3.2 + - - +
107A GLU* 2.8 31.7 + - - +
123A LEU* 4.0 15.5 - - + -
173A LEU* 4.1 8.5 - - + +
201A THR* 3.9 25.1 - - + +
204A HIS* 3.5 44.6 - - + -
205A VAL* 4.6 7.2 - - + -
208A LEU* 4.5 1.1 - - + -
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG 2.9 22.2 + - - +
101A LEU 3.9 0.9 - - - +
103A LEU* 1.3 73.1 - - - +
105A THR* 1.3 62.6 + - - +
107A GLU* 3.6 2.0 + - - -
108A SER* 3.1 24.6 + - - -
115A TYR* 3.7 19.5 - - + -
118A ALA* 3.7 8.2 - - - +
119A TYR* 3.7 33.0 - - + +
123A LEU* 3.9 12.6 - - + +
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Residues in contact with THR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.0 30.5 + - + +
16A LEU* 4.5 6.5 - - + +
101A LEU 2.7 23.5 + - - -
102A LEU 3.6 3.8 - - - -
104A ALA* 1.3 74.7 - - - +
106A MET* 1.3 59.8 + - - +
108A SER* 3.2 3.4 + - - -
109A MET* 2.9 50.0 + - + +
115A TYR* 3.6 18.5 + - - -
336A LEU* 4.3 12.9 - - + +
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Residues in contact with MET 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.8 30.0 - - + +
17A LYS 5.1 6.5 - - - +
18A ILE* 5.2 11.4 - - + -
19A GLN 5.7 1.8 - - - +
20A TYR* 6.3 0.9 - - + -
102A LEU* 2.9 38.2 + - + +
103A LEU* 3.8 4.3 - - - +
105A THR* 1.3 74.9 - - - +
107A GLU* 1.3 56.4 + - - +
109A MET* 3.8 1.3 - - - +
110A ASN* 2.9 36.4 + - + +
200A LEU* 3.6 49.8 - - + +
201A THR* 3.8 14.8 - - + -
204A HIS* 4.4 12.8 - - + +
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU 2.8 19.2 + - - +
104A ALA* 3.7 7.4 - - - +
106A MET* 1.3 75.2 - - - +
108A SER* 1.3 53.3 + - - +
110A ASN* 4.3 1.7 - - - +
111A GLY* 2.7 35.2 + - - -
113A LYS* 3.9 26.8 - - + +
118A ALA* 4.6 3.8 - - + -
122A ASP* 4.5 8.9 - - + +
123A LEU* 5.1 0.2 - - + -
171A PHE 4.2 0.7 - - - -
172A PRO* 3.3 24.4 - - + +
173A LEU* 2.9 42.2 + - + +
201A THR* 2.8 28.5 + - + +
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASN* 5.3 0.2 - - - +
104A ALA 3.1 16.0 + - - -
105A THR 3.7 3.6 - - - -
107A GLU* 1.3 79.5 - - - +
109A MET* 1.3 57.9 + - - +
112A GLY* 3.1 25.5 + - - -
113A LYS* 2.6 34.8 + - - +
115A TYR* 3.6 16.1 + - - -
118A ALA* 4.4 2.0 - - - +
335A PRO* 3.6 16.2 - - - +
336A LEU* 3.5 19.7 - - - +
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Residues in contact with MET 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 3.8 35.0 - - + +
18A ILE* 5.8 2.2 - - - -
42A ASN* 3.3 49.9 - - - +
43A PRO* 3.6 2.9 - - - +
49A LEU* 3.8 26.2 - - + -
105A THR* 2.9 28.3 + - + +
106A MET* 3.8 4.3 - - - +
108A SER* 1.3 78.9 + - - +
110A ASN* 1.3 58.9 + - - +
335A PRO* 5.7 1.1 - - - -
336A LEU* 4.1 23.2 - - + +
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.2 19.3 - - - +
41A PHE 3.5 7.3 + - - +
43A PRO* 3.2 17.4 - - - +
49A LEU* 4.1 6.6 - - + +
106A MET* 2.9 20.7 + - + +
107A GLU* 4.3 2.2 - - - +
109A MET* 1.3 74.2 - - - +
111A GLY* 1.3 58.8 + - - +
112A GLY 3.5 0.4 - - - -
197A GLN 2.9 22.5 + - - +
198A THR* 3.4 26.2 - - + +
200A LEU* 3.4 37.4 + - + +
201A THR* 4.9 2.1 + - + -
346A ILE* 4.1 2.6 - - - +
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Residues in contact with GLY 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PRO* 3.8 4.7 - - - +
107A GLU 2.7 20.5 + - - -
110A ASN* 1.3 74.3 - - - +
112A GLY* 1.3 62.4 + - - +
113A LYS* 3.2 6.4 + - - -
169A TRP 5.0 4.5 - - - +
172A PRO* 5.4 5.2 - - - -
198A THR* 4.1 9.9 - - - -
298A HIS* 4.0 13.7 + - - -
301A GLN* 5.0 3.3 + - - -
344A PRO 5.2 0.5 - - - +
346A ILE* 3.6 21.3 - - - +
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Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASN* 5.4 0.7 - - - -
43A PRO* 3.4 23.4 - - - +
44A ALA 5.3 0.4 - - - -
108A SER 3.1 9.3 + - - -
109A MET 5.1 0.2 - - - -
111A GLY* 1.3 76.8 - - - +
113A LYS* 1.3 59.6 + - - +
114A LEU 4.0 0.5 + - - -
298A HIS* 4.4 0.2 - - - -
299A GLN* 2.9 26.3 + - - -
335A PRO* 3.9 9.2 - - - -
343A GLY* 4.1 1.4 - - - -
344A PRO* 3.5 21.9 - - - +
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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