Contacts of the strand formed by residues 111 - 122 (chain I) in PDB entry 4N3E
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 GLY 111 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I SER 3.6 8.7 - - - -
13I PRO* 3.9 4.7 - - - -
14I ILE 3.3 17.3 - - - -
15I ALA* 3.9 3.6 - - - -
16I PRO* 4.1 3.3 - - - +
107I ALA* 3.5 4.9 - - - -
108I VAL 2.6 37.7 + - - -
109I GLY 3.2 1.8 - - - +
110I GLY* 1.3 78.1 - - - +
112I SER* 1.3 55.0 + - - -
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Residues in contact with SER 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I GLU* 3.2 5.4 - - - +
12I SER* 2.6 38.8 + - - +
14I ILE 2.6 22.6 + - - -
15I ALA 3.9 0.5 - - - -
16I PRO* 3.9 18.1 - - - +
19I LEU* 4.0 17.0 - - - +
105I LEU* 4.9 3.6 - - - -
106I GLU 3.3 17.0 - - - -
108I VAL* 4.1 10.1 - - - +
111I GLY* 1.3 71.6 - - - -
113I LYS* 1.3 65.7 + - - +
201I 2AN 5.3 0.9 - - - -
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Residues in contact with LYS 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLU* 6.5 0.4 - - + -
10I GLU 2.9 18.6 - - - +
11I GLU* 3.9 14.6 - - + +
105I LEU* 3.4 8.5 - - - +
106I GLU* 3.2 63.5 + - + +
107I ALA 4.7 0.4 + - - -
108I VAL* 3.4 26.4 - - + +
112I SER* 1.3 78.2 - - - +
114I GLY* 1.3 61.4 + - - +
201I 2AN 4.3 5.4 - - - -
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Residues in contact with GLY 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I LYS 4.0 0.2 - - - +
9I GLU* 3.2 5.0 - - - +
10I GLU* 2.8 33.7 + - - +
104I LYS 3.3 11.7 - - - -
105I LEU* 3.7 11.9 - - - -
113I LYS* 1.3 82.3 - - - +
115I LYS* 1.3 59.8 + - - -
116I ILE* 4.1 4.8 - - - +
201I 2AN 3.9 5.8 - - - -
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Residues in contact with LYS 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I VAL* 3.8 26.7 - - + -
8I LYS 3.5 14.1 - - - +
9I GLU* 4.0 20.2 + - + +
102I GLU 3.6 4.0 - - - +
103I VAL* 3.8 0.5 - - - -
104I LYS* 3.1 35.5 + - + +
114I GLY* 1.3 74.5 - - - -
116I ILE* 1.3 61.1 + - - +
117I THR* 4.2 7.7 + - - +
74J GLU* 5.8 1.0 + - - -
83J LYS* 5.3 10.9 - - - +
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Residues in contact with ILE 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ILE 3.9 1.0 - - - +
7I VAL* 3.4 1.7 - - - +
8I LYS* 2.8 55.9 + - + +
10I GLU* 4.5 3.6 - - + -
101I TYR* 5.3 0.7 - - + -
102I GLU 3.2 11.9 - - - +
103I VAL* 4.4 4.7 - - + -
105I LEU* 6.1 0.2 - - + -
114I GLY* 4.2 7.9 - - - +
115I LYS* 1.3 78.8 - - - +
117I THR* 1.3 61.5 + - - +
118I VAL* 3.9 19.6 - - + +
201I 2AN 3.1 86.1 - - + +
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Residues in contact with THR 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I THR* 3.6 26.9 - - + -
6I ILE 3.1 3.8 - - - -
7I VAL* 3.7 18.4 - - + +
100I VAL 3.8 1.6 - - - +
101I TYR* 3.6 0.9 - - - -
102I GLU* 3.0 56.1 + - - +
115I LYS* 4.9 7.6 + - - +
116I ILE* 1.3 74.9 + - - +
118I VAL* 1.3 65.7 + - - +
119I THR* 4.2 7.4 - - - +
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Residues in contact with VAL 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I TYR 3.7 1.2 - - - +
5I THR* 3.1 5.0 - - - +
6I ILE* 2.6 60.2 + - + +
8I LYS* 6.1 2.7 - - + -
99I VAL* 3.8 15.0 - - + -
100I VAL 3.6 3.1 - - - +
101I TYR* 3.5 38.4 - - + +
116I ILE* 3.9 18.4 - - + -
117I THR* 1.3 79.3 - - - +
119I THR* 1.3 63.4 + - - +
120I TYR* 3.8 16.6 - - + +
137I GLU* 5.7 3.1 - - + -
201I 2AN 5.6 2.0 - - + -
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Residues in contact with THR 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I ALA* 4.0 10.8 - - + -
4I TYR 3.5 2.9 - - - -
5I THR* 3.1 26.5 + - - +
99I VAL* 3.5 4.2 - - - +
100I VAL* 2.9 40.7 + - - -
102I GLU* 5.7 0.3 + - - -
117I THR* 4.2 7.3 - - - +
118I VAL* 1.3 75.4 - - - +
120I TYR* 1.3 62.2 + - - +
121I HIS* 3.1 37.1 - - + +
5J THR* 4.9 6.2 - - + +
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Residues in contact with TYR 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I ALA* 3.1 19.1 - - - +
4I TYR* 3.0 27.2 + - + +
6I ILE* 4.4 3.1 - - + +
96I ILE* 4.5 7.0 - - + -
98I LYS 3.8 3.1 - - - -
99I VAL* 3.8 24.9 - - + +
101I TYR* 4.9 1.6 + - - -
118I VAL* 3.8 25.6 - - + +
119I THR* 1.3 75.0 - - - +
121I HIS* 1.3 61.6 + - - +
122I PRO* 3.3 5.0 - - - +
128I VAL* 3.9 13.7 - - + +
132I GLU* 3.3 47.4 + - + +
133I VAL* 3.6 41.1 + - + -
136I GLY* 4.0 13.7 - - - -
137I GLU* 4.6 0.3 + - - +
202I 2AN 4.6 7.7 - + - -
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Residues in contact with HIS 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I ALA* 3.8 10.9 - - + +
96I ILE* 3.9 3.1 - - - +
97I GLU* 2.8 26.8 + - + +
98I LYS* 2.9 54.1 + - + +
100I VAL* 3.9 15.2 - - + +
119I THR* 3.1 39.5 - - + +
120I TYR* 1.3 70.5 - - - +
122I PRO* 1.3 67.6 - - + +
7J VAL* 4.9 18.2 - - + -
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Residues in contact with PRO 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I MET* 3.7 18.1 - - + +
2I ALA* 2.9 33.0 - - + +
3I ALA* 4.3 0.2 - - + -
95I ASN 3.5 14.6 - - - +
96I ILE* 4.3 3.4 - - + -
97I GLU* 3.9 4.8 - - - +
120I TYR 3.3 9.4 - - - +
121I HIS* 1.3 89.1 - - + +
123I LYS* 1.3 63.4 + - - +
124I PRO* 3.9 3.1 - - - +
126I CYS 3.7 15.5 - - - +
127I THR* 4.3 6.5 - - - +
128I VAL* 3.8 21.5 - - + +
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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